text
stringlengths 170
217
| clean_label
stringclasses 2
values | Name
stringlengths 24
50
| Assembly
stringclasses 1
value | chrom
stringclasses 25
values | pos
stringlengths 3
9
| ref
stringclasses 4
values | alt
stringclasses 4
values | gnomad_af
float64 0
1
|
|---|---|---|---|---|---|---|---|---|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: PROC
Variant: NM_000312.4(PROC):c.436G>T (p.Gly146Cys)
### Response:
|
Pathogenic
|
NM_000312.4(PROC):c.436G>T (p.Gly146Cys)
|
GRCh38
|
2
|
127423309
|
G
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: ADGRV1
Variant: NM_032119.4(ADGRV1):c.6314T>C (p.Ile2105Thr)
### Response:
|
Benign
|
NM_032119.4(ADGRV1):c.6314T>C (p.Ile2105Thr)
|
GRCh38
|
5
|
90685819
|
T
|
C
| 0.000005
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: SYNGAP1
Variant: NM_006772.3(SYNGAP1):c.1898T>C (p.Leu633Pro)
### Response:
|
Pathogenic
|
NM_006772.3(SYNGAP1):c.1898T>C (p.Leu633Pro)
|
GRCh38
|
6
|
33440950
|
T
|
C
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: RGR
Variant: NM_001012720.2(RGR):c.273C>T (p.His91=)
### Response:
|
Benign
|
NM_001012720.2(RGR):c.273C>T (p.His91=)
|
GRCh38
|
10
|
84248958
|
C
|
T
| 0.000032
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: MUTYH
Variant: NM_001048174.2(MUTYH):c.1021G>T (p.Glu341Ter)
### Response:
|
Pathogenic
|
NM_001048174.2(MUTYH):c.1021G>T (p.Glu341Ter)
|
GRCh38
|
1
|
45331742
|
C
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: HPS4
Variant: NM_022081.6(HPS4):c.1234C>T (p.Leu412=)
### Response:
|
Benign
|
NM_022081.6(HPS4):c.1234C>T (p.Leu412=)
|
GRCh38
|
22
|
26464396
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CCDC39
Variant: NM_181426.2(CCDC39):c.493C>T (p.Gln165Ter)
### Response:
|
Pathogenic
|
NM_181426.2(CCDC39):c.493C>T (p.Gln165Ter)
|
GRCh38
|
3
|
180660593
|
G
|
A
| 0.000002
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: EGFR
Variant: NM_005228.5(EGFR):c.3522G>A (p.Gln1174=)
### Response:
|
Benign
|
NM_005228.5(EGFR):c.3522G>A (p.Gln1174=)
|
GRCh38
|
7
|
55205506
|
G
|
A
| 0.000003
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: FOXA2
Variant: NM_021784.5(FOXA2):c.619C>T (p.Gln207Ter)
### Response:
|
Pathogenic
|
NM_021784.5(FOXA2):c.619C>T (p.Gln207Ter)
|
GRCh38
|
20
|
22582623
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: LRPPRC
Variant: NM_133259.4(LRPPRC):c.30G>A (p.Trp10Ter)
### Response:
|
Pathogenic
|
NM_133259.4(LRPPRC):c.30G>A (p.Trp10Ter)
|
GRCh38
|
2
|
43995918
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: SFTPC
Variant: NM_001317778.2(SFTPC):c.218T>C (p.Ile73Thr)
### Response:
|
Pathogenic
|
NM_001317778.2(SFTPC):c.218T>C (p.Ile73Thr)
|
GRCh38
|
8
|
22163096
|
T
|
C
| 0.000003
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CPS1
Variant: NM_001875.5(CPS1):c.947+1G>A
### Response:
|
Pathogenic
|
NM_001875.5(CPS1):c.947+1G>A
|
GRCh38
|
2
|
210590907
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: BARD1
Variant: NM_000465.4(BARD1):c.1314+1G>A
### Response:
|
Pathogenic
|
NM_000465.4(BARD1):c.1314+1G>A
|
GRCh38
|
2
|
214780559
|
C
|
T
| 0.000002
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: ABCC8
Variant: NM_000352.6(ABCC8):c.674T>C (p.Leu225Pro)
### Response:
|
Pathogenic
|
NM_000352.6(ABCC8):c.674T>C (p.Leu225Pro)
|
GRCh38
|
11
|
17461731
|
A
|
G
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: STXBP2
Variant: NM_006949.4(STXBP2):c.1138G>T (p.Glu380Ter)
### Response:
|
Pathogenic
|
NM_006949.4(STXBP2):c.1138G>T (p.Glu380Ter)
|
GRCh38
|
19
|
7644644
|
G
|
T
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: LAMA5
Variant: NM_005560.6(LAMA5):c.6804C>T (p.Thr2268=)
### Response:
|
Benign
|
NM_005560.6(LAMA5):c.6804C>T (p.Thr2268=)
|
GRCh38
|
20
|
62319751
|
G
|
A
| 0.000157
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: VPS13B
Variant: NM_152564.5(VPS13B):c.11216-1G>A
### Response:
|
Pathogenic
|
NM_152564.5(VPS13B):c.11216-1G>A
|
GRCh38
|
8
|
99868288
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CDH23
Variant: NM_022124.6(CDH23):c.2025C>T (p.Ala675=)
### Response:
|
Benign
|
NM_022124.6(CDH23):c.2025C>T (p.Ala675=)
|
GRCh38
|
10
|
71687685
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: ACADVL
Variant: NM_000018.4(ACADVL):c.839C>T (p.Thr280Ile)
### Response:
|
Pathogenic
|
NM_000018.4(ACADVL):c.839C>T (p.Thr280Ile)
|
GRCh38
|
17
|
7222263
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CSF1R
Variant: NM_001288705.3(CSF1R):c.1991A>T (p.Glu664Val)
### Response:
|
Pathogenic
|
NM_001288705.3(CSF1R):c.1991A>T (p.Glu664Val)
|
GRCh38
|
5
|
150059841
|
T
|
A
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TAB2
Variant: NM_001292034.3(TAB2):c.1858+9C>A
### Response:
|
Benign
|
NM_001292034.3(TAB2):c.1858+9C>A
|
GRCh38
|
6
|
149398071
|
C
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: LIFR
Variant: NM_001127671.2(LIFR):c.1566G>A (p.Trp522Ter)
### Response:
|
Pathogenic
|
NM_001127671.2(LIFR):c.1566G>A (p.Trp522Ter)
|
GRCh38
|
5
|
38502671
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: LDHA
Variant: NM_005566.4(LDHA):c.-25+130A>C
### Response:
|
Benign
|
NM_005566.4(LDHA):c.-25+130A>C
|
GRCh38
|
11
|
18394766
|
A
|
C
| 0.00883
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: SLC22A5
Variant: NM_003060.4(SLC22A5):c.228G>A (p.Glu76=)
### Response:
|
Benign
|
NM_003060.4(SLC22A5):c.228G>A (p.Glu76=)
|
GRCh38
|
5
|
132370200
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CEP290
Variant: NM_025114.4(CEP290):c.6838A>T (p.Lys2280Ter)
### Response:
|
Pathogenic
|
NM_025114.4(CEP290):c.6838A>T (p.Lys2280Ter)
|
GRCh38
|
12
|
88055698
|
T
|
A
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: PGM3
Variant: NM_015599.3(PGM3):c.-2-648A>G
### Response:
|
Benign
|
NM_015599.3(PGM3):c.-2-648A>G
|
GRCh38
|
6
|
83191662
|
T
|
C
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TRIOBP
Variant: NM_001039141.3(TRIOBP):c.2968C>T (p.Arg990Ter)
### Response:
|
Pathogenic
|
NM_001039141.3(TRIOBP):c.2968C>T (p.Arg990Ter)
|
GRCh38
|
22
|
37725524
|
C
|
T
| 0.00001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: G6PC3
Variant: NM_138387.4(G6PC3):c.482G>A (p.Arg161Gln)
### Response:
|
Pathogenic
|
NM_138387.4(G6PC3):c.482G>A (p.Arg161Gln)
|
GRCh38
|
17
|
44075034
|
G
|
A
| 0.000008
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: ABCA12
Variant: NM_173076.3(ABCA12):c.1782+7T>C
### Response:
|
Benign
|
NM_173076.3(ABCA12):c.1782+7T>C
|
GRCh38
|
2
|
215018001
|
A
|
G
| 0.000004
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: HLCS
Variant: NM_001352514.2(HLCS):c.1960+5G>A
### Response:
|
Pathogenic
|
NM_001352514.2(HLCS):c.1960+5G>A
|
GRCh38
|
21
|
36767213
|
C
|
T
| 0.000061
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TREX1
Variant: NM_033629.6(TREX1):c.318C>T (p.Asn106=)
### Response:
|
Benign
|
NM_033629.6(TREX1):c.318C>T (p.Asn106=)
|
GRCh38
|
3
|
48466973
|
C
|
T
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CYP11B2
Variant: NM_000498.3(CYP11B2):c.501C>T (p.Asp167=)
### Response:
|
Benign
|
NM_000498.3(CYP11B2):c.501C>T (p.Asp167=)
|
GRCh38
|
8
|
142915140
|
G
|
A
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: ZNF469
Variant: NM_001367624.2(ZNF469):c.1338C>G (p.Ala446=)
### Response:
|
Benign
|
NM_001367624.2(ZNF469):c.1338C>G (p.Ala446=)
|
GRCh38
|
16
|
88428808
|
C
|
G
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CDH1
Variant: NM_004360.5(CDH1):c.687+66A>G
### Response:
|
Benign
|
NM_004360.5(CDH1):c.687+66A>G
|
GRCh38
|
16
|
68808914
|
A
|
G
| 0.001451
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TTN
Variant: NM_001267550.2(TTN):c.55732+17A>C
### Response:
|
Benign
|
NM_001267550.2(TTN):c.55732+17A>C
|
GRCh38
|
2
|
178601248
|
T
|
G
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: DGAT1
Variant: NM_012079.6(DGAT1):c.1020G>A (p.Trp340Ter)
### Response:
|
Pathogenic
|
NM_012079.6(DGAT1):c.1020G>A (p.Trp340Ter)
|
GRCh38
|
8
|
144317407
|
C
|
T
| 0.000017
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TTN
Variant: NM_001267550.2(TTN):c.21621C>T (p.Tyr7207=)
### Response:
|
Benign
|
NM_001267550.2(TTN):c.21621C>T (p.Tyr7207=)
|
GRCh38
|
2
|
178723479
|
G
|
A
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: FAIM2
Variant: NM_012306.4(FAIM2):c.520G>A (p.Val174Ile)
### Response:
|
Benign
|
NM_012306.4(FAIM2):c.520G>A (p.Val174Ile)
|
GRCh38
|
12
|
49890688
|
C
|
T
| 0.000023
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: COL6A1
Variant: NM_001848.3(COL6A1):c.1336-12G>A
### Response:
|
Benign
|
NM_001848.3(COL6A1):c.1336-12G>A
|
GRCh38
|
21
|
45994155
|
G
|
A
| 0.000032
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: USH2A
Variant: NM_206933.4(USH2A):c.6325+2T>G
### Response:
|
Pathogenic
|
NM_206933.4(USH2A):c.6325+2T>G
|
GRCh38
|
1
|
216046429
|
A
|
C
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: COL4A5
Variant: NM_033380.3(COL4A5):c.2387G>A (p.Gly796Glu)
### Response:
|
Pathogenic
|
NM_033380.3(COL4A5):c.2387G>A (p.Gly796Glu)
|
GRCh38
|
X
|
108606884
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: FBN1
Variant: NM_000138.5(FBN1):c.2961C>G (p.Ala987=)
### Response:
|
Benign
|
NM_000138.5(FBN1):c.2961C>G (p.Ala987=)
|
GRCh38
|
15
|
48489972
|
G
|
C
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: ANO10
Variant: NM_018075.5(ANO10):c.*432G>T
### Response:
|
Benign
|
NM_018075.5(ANO10):c.*432G>T
|
GRCh38
|
3
|
43366474
|
C
|
A
| 0.011614
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TTN
Variant: NM_001267550.2(TTN):c.39127+15T>A
### Response:
|
Benign
|
NM_001267550.2(TTN):c.39127+15T>A
|
GRCh38
|
2
|
178652443
|
A
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: HMOX1
Variant: NM_002133.3(HMOX1):c.610A>T (p.Lys204Ter)
### Response:
|
Pathogenic
|
NM_002133.3(HMOX1):c.610A>T (p.Lys204Ter)
|
GRCh38
|
22
|
35387150
|
A
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: GATM
Variant: NM_001482.3(GATM):c.814-9T>C
### Response:
|
Benign
|
NM_001482.3(GATM):c.814-9T>C
|
GRCh38
|
15
|
45366219
|
A
|
G
| 0.000013
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: IQSEC2
Variant: NM_001111125.3(IQSEC2):c.2854C>T (p.Gln952Ter)
### Response:
|
Pathogenic
|
NM_001111125.3(IQSEC2):c.2854C>T (p.Gln952Ter)
|
GRCh38
|
X
|
53243367
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: APOA1
Variant: NM_000039.3(APOA1):c.693C>G (p.Ala231=)
### Response:
|
Benign
|
NM_000039.3(APOA1):c.693C>G (p.Ala231=)
|
GRCh38
|
11
|
116835919
|
G
|
C
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: AFF4
Variant: NM_014423.4(AFF4):c.2307+18G>A
### Response:
|
Benign
|
NM_014423.4(AFF4):c.2307+18G>A
|
GRCh38
|
5
|
132896305
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: KMT2D
Variant: NM_003482.4(KMT2D):c.10378C>T (p.Gln3460Ter)
### Response:
|
Pathogenic
|
NM_003482.4(KMT2D):c.10378C>T (p.Gln3460Ter)
|
GRCh38
|
12
|
49034644
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: EIF2AK4
Variant: NM_001013703.4(EIF2AK4):c.860-1G>A
### Response:
|
Pathogenic
|
NM_001013703.4(EIF2AK4):c.860-1G>A
|
GRCh38
|
15
|
39965685
|
G
|
A
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CFTR
Variant: NM_000492.4(CFTR):c.3139+11G>C
### Response:
|
Benign
|
NM_000492.4(CFTR):c.3139+11G>C
|
GRCh38
|
7
|
117610680
|
G
|
C
| 0.000002
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CPT1A
Variant: NM_001876.4(CPT1A):c.1716G>A (p.Leu572=)
### Response:
|
Benign
|
NM_001876.4(CPT1A):c.1716G>A (p.Leu572=)
|
GRCh38
|
11
|
68773289
|
C
|
T
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: OBSCN
Variant: NM_001386125.1(OBSCN):c.8467G>A (p.Ala2823Thr)
### Response:
|
Benign
|
NM_001386125.1(OBSCN):c.8467G>A (p.Ala2823Thr)
|
GRCh38
|
1
|
228279228
|
G
|
A
| 0.000044
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: SLC1A2
Variant: NM_004171.4(SLC1A2):c.92G>A (p.Arg31Gln)
### Response:
|
Benign
|
NM_004171.4(SLC1A2):c.92G>A (p.Arg31Gln)
|
GRCh38
|
11
|
35317442
|
C
|
T
| 0.000211
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: SMARCA4
Variant: NM_003072.5(SMARCA4):c.2164C>T (p.Gln722Ter)
### Response:
|
Pathogenic
|
NM_003072.5(SMARCA4):c.2164C>T (p.Gln722Ter)
|
GRCh38
|
19
|
11010421
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: NAA10
Variant: NM_003491.4(NAA10):c.236G>A (p.Arg79His)
### Response:
|
Pathogenic
|
NM_003491.4(NAA10):c.236G>A (p.Arg79His)
|
GRCh38
|
X
|
153932421
|
C
|
T
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: ERCC6L2
Variant: NM_020207.7(ERCC6L2):c.2954A>T (p.Asp985Val)
### Response:
|
Benign
|
NM_020207.7(ERCC6L2):c.2954A>T (p.Asp985Val)
|
GRCh38
|
9
|
95972705
|
A
|
T
| 0.00007
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: VPS13A
Variant: NM_033305.3(VPS13A):c.2428-6T>C
### Response:
|
Benign
|
NM_033305.3(VPS13A):c.2428-6T>C
|
GRCh38
|
9
|
77273274
|
T
|
C
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TTN
Variant: NM_001267550.2(TTN):c.42024+6T>C
### Response:
|
Benign
|
NM_001267550.2(TTN):c.42024+6T>C
|
GRCh38
|
2
|
178635159
|
A
|
G
| 0.000567
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: BRCA2
Variant: NM_000059.4(BRCA2):c.8058T>A (p.Leu2686=)
### Response:
|
Benign
|
NM_000059.4(BRCA2):c.8058T>A (p.Leu2686=)
|
GRCh38
|
13
|
32363260
|
T
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: EVC
Variant: NM_153717.3(EVC):c.822G>A (p.Lys274=)
### Response:
|
Benign
|
NM_153717.3(EVC):c.822G>A (p.Lys274=)
|
GRCh38
|
4
|
5745224
|
G
|
A
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: ELP1
Variant: NM_003640.5(ELP1):c.3573-1G>A
### Response:
|
Pathogenic
|
NM_003640.5(ELP1):c.3573-1G>A
|
GRCh38
|
9
|
108878751
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: PKHD1
Variant: NM_138694.4(PKHD1):c.10228C>T (p.Gln3410Ter)
### Response:
|
Pathogenic
|
NM_138694.4(PKHD1):c.10228C>T (p.Gln3410Ter)
|
GRCh38
|
6
|
51659898
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: LAMC2
Variant: NM_005562.3(LAMC2):c.2778T>G (p.Arg926=)
### Response:
|
Benign
|
NM_005562.3(LAMC2):c.2778T>G (p.Arg926=)
|
GRCh38
|
1
|
183238330
|
T
|
G
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: USH2A
Variant: NM_206933.4(USH2A):c.5519G>T (p.Gly1840Val)
### Response:
|
Pathogenic
|
NM_206933.4(USH2A):c.5519G>T (p.Gly1840Val)
|
GRCh38
|
1
|
216078142
|
C
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: PRR21
Variant: NC_000002.12:g.240042159C>G
### Response:
|
Benign
|
NC_000002.12:g.240042159C>G
|
GRCh38
|
2
|
240042159
|
C
|
G
| 0.006606
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: FREM1
Variant: NM_001379081.2(FREM1):c.5761C>T (p.Gln1921Ter)
### Response:
|
Pathogenic
|
NM_001379081.2(FREM1):c.5761C>T (p.Gln1921Ter)
|
GRCh38
|
9
|
14748436
|
G
|
A
| 0.00001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CYP1B1
Variant: NM_000104.4(CYP1B1):c.490C>T (p.Gln164Ter)
### Response:
|
Pathogenic
|
NM_000104.4(CYP1B1):c.490C>T (p.Gln164Ter)
|
GRCh38
|
2
|
38074899
|
G
|
A
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: ATR
Variant: NM_001184.4(ATR):c.7365A>C (p.Ser2455=)
### Response:
|
Benign
|
NM_001184.4(ATR):c.7365A>C (p.Ser2455=)
|
GRCh38
|
3
|
142459096
|
T
|
G
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: DSG2
Variant: NM_001943.5(DSG2):c.1970G>A (p.Trp657Ter)
### Response:
|
Pathogenic
|
NM_001943.5(DSG2):c.1970G>A (p.Trp657Ter)
|
GRCh38
|
18
|
31541283
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: PTCH2
Variant: NM_003738.5(PTCH2):c.3115-212G>A
### Response:
|
Benign
|
NM_003738.5(PTCH2):c.3115-212G>A
|
GRCh38
|
1
|
44823597
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: C1QB
Variant: NM_001378156.1(C1QB):c.267C>G (p.Pro89=)
### Response:
|
Benign
|
NM_001378156.1(C1QB):c.267C>G (p.Pro89=)
|
GRCh38
|
1
|
22660897
|
C
|
G
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: SBF2
Variant: NM_030962.4(SBF2):c.56-1G>A
### Response:
|
Pathogenic
|
NM_030962.4(SBF2):c.56-1G>A
|
GRCh38
|
11
|
10193988
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: COL5A1
Variant: NM_000093.5(COL5A1):c.1633C>T (p.Gln545Ter)
### Response:
|
Pathogenic
|
NM_000093.5(COL5A1):c.1633C>T (p.Gln545Ter)
|
GRCh38
|
9
|
134750853
|
C
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: HBA2
Variant: NM_000517.6(HBA2):c.200T>C (p.Leu67Pro)
### Response:
|
Pathogenic
|
NM_000517.6(HBA2):c.200T>C (p.Leu67Pro)
|
GRCh38
|
16
|
173229
|
T
|
C
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: F2
Variant: NM_000506.5(F2):c.261C>T (p.Tyr87=)
### Response:
|
Benign
|
NM_000506.5(F2):c.261C>T (p.Tyr87=)
|
GRCh38
|
11
|
46720543
|
C
|
T
| 0.000047
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: AGL
Variant: NM_000642.3(AGL):c.3700+236G>A
### Response:
|
Benign
|
NM_000642.3(AGL):c.3700+236G>A
|
GRCh38
|
1
|
99903030
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TSHR
Variant: NM_000369.5(TSHR):c.1349G>A (p.Arg450His)
### Response:
|
Pathogenic
|
NM_000369.5(TSHR):c.1349G>A (p.Arg450His)
|
GRCh38
|
14
|
81143407
|
G
|
A
| 0.000111
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CLN3
Variant: NM_001042432.2(CLN3):c.45G>A (p.Glu15=)
### Response:
|
Benign
|
NM_001042432.2(CLN3):c.45G>A (p.Glu15=)
|
GRCh38
|
16
|
28491715
|
C
|
T
| 0.000926
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: PDGFRA
Variant: NM_006206.6(PDGFRA):c.2537A>T (p.Asp846Val)
### Response:
|
Pathogenic
|
NM_006206.6(PDGFRA):c.2537A>T (p.Asp846Val)
|
GRCh38
|
4
|
54285938
|
A
|
T
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: DARS2
Variant: NM_018122.5(DARS2):c.1440G>A (p.Trp480Ter)
### Response:
|
Pathogenic
|
NM_018122.5(DARS2):c.1440G>A (p.Trp480Ter)
|
GRCh38
|
1
|
173853444
|
G
|
A
| 0.000004
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: KMT2A
Variant: NM_001197104.2(KMT2A):c.10835+13A>G
### Response:
|
Benign
|
NM_001197104.2(KMT2A):c.10835+13A>G
|
GRCh38
|
11
|
118507622
|
A
|
G
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: PIK3C2A
Variant: NM_002645.4(PIK3C2A):c.493C>T (p.Gln165Ter)
### Response:
|
Pathogenic
|
NM_002645.4(PIK3C2A):c.493C>T (p.Gln165Ter)
|
GRCh38
|
11
|
17169249
|
G
|
A
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: AGPS
Variant: NM_003659.4(AGPS):c.1476-5T>C
### Response:
|
Benign
|
NM_003659.4(AGPS):c.1476-5T>C
|
GRCh38
|
2
|
177505501
|
T
|
C
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CAPN3
Variant: NM_000070.3(CAPN3):c.632+263A>G
### Response:
|
Benign
|
NM_000070.3(CAPN3):c.632+263A>G
|
GRCh38
|
15
|
42388149
|
A
|
G
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: LARGE1
Variant: NM_133642.5(LARGE1):c.788-8C>T
### Response:
|
Benign
|
NM_133642.5(LARGE1):c.788-8C>T
|
GRCh38
|
22
|
33432273
|
G
|
A
| 0.000022
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: PIGG
Variant: NM_001127178.3(PIGG):c.931C>T (p.Gln311Ter)
### Response:
|
Pathogenic
|
NM_001127178.3(PIGG):c.931C>T (p.Gln311Ter)
|
GRCh38
|
4
|
516002
|
C
|
T
| 0.000001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: PEX1
Variant: NM_000466.3(PEX1):c.1359+13A>G
### Response:
|
Benign
|
NM_000466.3(PEX1):c.1359+13A>G
|
GRCh38
|
7
|
92513835
|
T
|
C
| 0.000006
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TGIF1
Variant: NM_003244.4(TGIF1):c.188C>G (p.Pro63Arg)
### Response:
|
Pathogenic
|
NM_003244.4(TGIF1):c.188C>G (p.Pro63Arg)
|
GRCh38
|
18
|
3456525
|
C
|
G
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: VRK1
Variant: NM_003384.3(VRK1):c.897T>C (p.Ile299=)
### Response:
|
Benign
|
NM_003384.3(VRK1):c.897T>C (p.Ile299=)
|
GRCh38
|
14
|
96860564
|
T
|
C
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: MYO7A
Variant: NM_000260.4(MYO7A):c.6052-19C>G
### Response:
|
Benign
|
NM_000260.4(MYO7A):c.6052-19C>G
|
GRCh38
|
11
|
77211133
|
C
|
G
| 0.000004
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: RPL5
Variant: NM_000969.5(RPL5):c.794+121G>A
### Response:
|
Benign
|
NM_000969.5(RPL5):c.794+121G>A
|
GRCh38
|
1
|
92840760
|
G
|
A
| 0.669005
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: RIT1
Variant: NM_006912.6(RIT1):c.486G>A (p.Glu162=)
### Response:
|
Benign
|
NM_006912.6(RIT1):c.486G>A (p.Glu162=)
|
GRCh38
|
1
|
155900562
|
C
|
T
| 0.000003
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: SHROOM2
Variant: NM_001649.4(SHROOM2):c.2859A>G (p.Ala953=)
### Response:
|
Benign
|
NM_001649.4(SHROOM2):c.2859A>G (p.Ala953=)
|
GRCh38
|
X
|
9898258
|
A
|
G
| 0.001652
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: UNC13D
Variant: NM_199242.3(UNC13D):c.883C>T (p.Gln295Ter)
### Response:
|
Pathogenic
|
NM_199242.3(UNC13D):c.883C>T (p.Gln295Ter)
|
GRCh38
|
17
|
75840086
|
G
|
A
| 0
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: DUOX2
Variant: NM_001363711.2(DUOX2):c.3565+9C>T
### Response:
|
Benign
|
NM_001363711.2(DUOX2):c.3565+9C>T
|
GRCh38
|
15
|
45098000
|
G
|
A
| 0.000025
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TTC21B
Variant: NM_024753.5(TTC21B):c.1854G>A (p.Ser618=)
### Response:
|
Benign
|
NM_024753.5(TTC21B):c.1854G>A (p.Ser618=)
|
GRCh38
|
2
|
165917302
|
C
|
T
| 0.000029
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: TNNI2
Variant: NM_003282.4(TNNI2):c.423G>C (p.Leu141=)
### Response:
|
Benign
|
NM_003282.4(TNNI2):c.423G>C (p.Leu141=)
|
GRCh38
|
11
|
1841177
|
G
|
C
| 0.00001
|
Below is a biological context regarding a genetic variant. Determine if it is Pathogenic or Benign.
### Input:
Gene: CHAT
Variant: NM_020549.5(CHAT):c.1516G>T (p.Val506Leu)
### Response:
|
Pathogenic
|
NM_020549.5(CHAT):c.1516G>T (p.Val506Leu)
|
GRCh38
|
10
|
49651888
|
G
|
T
| 0.000001
|
End of preview. Expand
in Data Studio
This uploaded dataset is a sample data of 12k rows for train and 1.2k for test to get idea of the dataset used in making of PathoPreter
https://huggingface.co/YADAV0206/PathoPreter-4B-SNV-Pathogen-ClinVar-gnomAD
The model's full training dataset contains approximately 144k pathogenic variants and 1.05 million benign variants, for a total of about 1.2 million samples and Testing have 55k total different samples with 11 seperate ablations tests (on same 55k rows) making around 12*55k=660k”
To get the Dataset contact Rohit Yadav
📦 Dataset Availability
Dataset Construction and Availability:
The datasets used to train and evaluate PathoPreter (including large-scale ClinVar-derived SNV corpora, controlled ablation test suites, and robustness evaluation datasets) were fully constructed in-house using publicly available, permissively licensed genomic resources such as ClinVar and gnomAD. All upstream sources are properly credited and explicitly permit commercial use and redistribution.
Significant original engineering and curation effort was applied beyond raw data usage. This included large-scale extraction, normalization, schema unification, quality control, deduplication, and strict train–test disjointness enforcement. Approximately 8 million raw ClinVar variants and ~250 GB of gnomAD VCF data were processed and merged into production-grade Parquet datasets optimized for large-scale analytics, machine learning training, and downstream integration.
The end-to-end data construction process required approximately 150 hours of compute time and over 250 hours of expert engineering and curation work. The resulting datasets constitute a high-value derived data asset, distinct from the original source distributions.
These datasets are available for licensed distribution to startups, enterprises, and research organizations for use in applied genomics, AI/ML model development, benchmarking, variant prioritization workflows, and internal research. Commercial licensing, redistribution terms, and support options are available upon request.
Available components include:(in Parquet and CSV both)
- Large-scale ClinVar-style SNV training dataset
- Held-out test set with identical variants across ablations
- Controlled ablation datasets (signal removal studies)
- Fake-variant's robustness evaluation dataset (see below why is it important in FAKE VARIANT ROBUSTNESS TEST)
- Balanced CSV subsets suitable for classical ML training
- Data audit and leakage-verification scripts
If you are interested in:
- dataset licensing
- research or industry use
- collaboration or benchmarking
- reproducing or extending this work
please contact:
Rohit Yadav
Requests are evaluated on a case-by-case basis.
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