chr3:10183534:G>A Detail (hg19) (VHL)

Information

Genome

Assembly Position
hg19 chr3:10,183,534-10,183,534
hg38 chr3:10,141,850-10,141,850 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000551.3:c.3G>A NP_000542.1:p.?
NM_198156.2:c.3G>A NP_937799.1:p.?
Ensemble ENST00000256474.3:c.3G>A ENST00000256474.3:p.?
Summary

MGeND

Clinical significance not provided
Variant entry 6
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 608537 OMIM
HGNC 12687 HGNC
Ensembl ENSG00000134086 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv11440245 TogoVar
COSMIC COSM14367 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
not provided stomach, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided bronchus or lung, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2023-08-15 criteria provided, single submitter not specified germline Detail
Uncertain significance 2023-12-13 criteria provided, multiple submitters, no conflicts Von Hippel-Lindau syndrome germline unknown Detail
Uncertain significance 2024-01-30 criteria provided, single submitter Chuvash polycythemia,Von Hippel-Lindau syndrome germline Detail
Uncertain significance 2024-01-30 criteria provided, single submitter Chuvash polycythemia,Von Hippel-Lindau syndrome germline Detail
Conflicting interpretations of pathogenicity 2022-10-27 criteria provided, conflicting interpretations Hereditary cancer-predisposing syndrome germline Detail
Uncertain significance 2023-04-28 criteria provided, single submitter not provided germline Detail
Uncertain significance 2022-04-27 criteria provided, single submitter nonpapillary renal cell carcinoma,Von Hippel-Lindau syndrome,pheochromocytoma,Chuvash polycythemia unknown Detail
Uncertain significance 2022-04-27 criteria provided, single submitter nonpapillary renal cell carcinoma,Von Hippel-Lindau syndrome,pheochromocytoma,Chuvash polycythemia unknown Detail
Uncertain significance 2022-04-27 criteria provided, single submitter nonpapillary renal cell carcinoma,Von Hippel-Lindau syndrome,pheochromocytoma,Chuvash polycythemia unknown Detail
Uncertain significance 2022-04-27 criteria provided, single submitter nonpapillary renal cell carcinoma,Von Hippel-Lindau syndrome,pheochromocytoma,Chuvash polycythemia unknown Detail
CIViC
Disease Drug EL ET ED CS VO TR Pubmed Links
von Hippel-Lindau disease E Predisposing Supports Uncertain Significance Somatic 2 11505222 Detail
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
Mutation detected in one case. Case shows clear-cell renal cell carcinoma. This case also harbored a... CIViC Evidence Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND not specified ClinVar Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND Von Hippel-Lindau syndrome ClinVar Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND not provided ClinVar Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.3G>A (p.Met1Ile) AND multiple conditions ClinVar Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs578091032 dbSNP
Genome
hg19
Position
chr3:10,183,534-10,183,534
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1169
Mean of sample read depth (HGVD)
24.65
Standard deviation of sample read depth (HGVD)
9.98
Number of reference allele (HGVD)
2336
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.55431993156544E-4
Gene Symbol (HGVD)
VHL
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs578091032
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
346
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
11442
Allele Counts in All Race (ExAC)
2
Heterozygous Counts in All Race (ExAC)
2
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.7479461632581716E-4
Variant (CIViC) (CIViC Variant)
M1? (c.3G>A)
Transcript 1 (CIViC Variant)
ENST00000256474.2
Variant URL (CIViC Variant)
https://civic.genome.wustl.edu/links/variants/848
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