chr3:52437206:G>A Detail (hg19) (BAP1)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

Assembly	Position
hg19	chr3:52,437,206-52,437,206
hg38	chr3:52,403,190-52,403,190 View the variant detail on this assembly version.

HGVS

BAP1

Type	Transcript	Protein
RefSeq	NM_004656.3:c.1838C>T	NP_004647.1:p.Thr613Met
Ensemble	ENST00000296288.9:c.1784C>T	ENST00000296288.9:p.Thr595Met
	ENST00000460680.6:c.1838C>T	ENST00000460680.6:p.Thr613Met

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

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

Prediction

ClinVar

Clinical Significance	Benign Likely benign
Review star
Show details

Links

BAP1

Type	Database	ID	Link
Gene	MIM	603089	OMIM
	HGNC	950	HGNC
	Ensembl	ENSG00000163930	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar
	COSMIC	COSM5931223	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2023-08-15	criteria provided, multiple submitters, no conflicts	not specified	germline unknown	Detail
Benign Likely benign	2024-01-31	criteria provided, multiple submitters, no conflicts	BAP1-related tumor predisposition syndrome	germline	Detail
Benign	2018-08-06	criteria provided, multiple submitters, no conflicts	Hereditary cancer-predisposing syndrome	germline	Detail
Benign	2021-05-13	criteria provided, single submitter	not provided	germline	Detail
Benign	2023-07-07	criteria provided, single submitter	Melanoma, uveal, susceptibility to, 2	germline	Detail

CIViC

[No Data.]

DisGeNET

[No Data.]

Annotation

Annotations

Descrption	Source	Links
NM_004656.4(BAP1):c.1838C>T (p.Thr613Met) AND not specified	ClinVar	Detail
NM_004656.4(BAP1):c.1838C>T (p.Thr613Met) AND BAP1-related tumor predisposition syndrome	ClinVar	Detail
NM_004656.4(BAP1):c.1838C>T (p.Thr613Met) AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_004656.4(BAP1):c.1838C>T (p.Thr613Met) AND not provided	ClinVar	Detail
NM_004656.4(BAP1):c.1838C>T (p.Thr613Met) AND Melanoma, uveal, susceptibility to, 2	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: rs35448940 dbSNP
Genome: hg19
Position: chr3:52,437,206-52,437,206
Variant Type: snv
Reference Allele: G
Alternative Allele: A
East Asian Chromosome Counts (ExAC): 8652
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): 121364
Allele Counts in All Race (ExAC): 142
Heterozygous Counts in All Race (ExAC): 140
Homozygous Counts in All Race (ExAC): 1
Allele Frequency in All Race (ExAC): 0.0011700339474638279

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