chr16:89919532:G>A Detail (hg38) (MC1R)

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Information

Genome

Assembly	Position
hg19	chr16:89,985,940-89,985,940 View the variant detail on this assembly version.
hg38	chr16:89,919,532-89,919,532

Summary

Links

Type	Database	ID	Link
Gene	MIM	155555	OMIM
	HGNC	6929	HGNC
	Ensembl	ENSG00000258839	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv56656290	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
association	2006-04-01	no assertion criteria provided	Skin/hair/eye pigmentation 2, red hair/fair skin	germline	Detail
association	2006-04-01	no assertion criteria provided	Skin/hair/eye pigmentation 2, blond hair/fair skin	germline	Detail
Benign		criteria provided, single submitter	not specified	germline	Detail
Benign	2024-02-01	criteria provided, multiple submitters, no conflicts	Melanoma, cutaneous malignant, susceptibility to, 5	germline	Detail
Benign	2019-03-01	criteria provided, single submitter	not provided	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.284	melanoma	Furthermore, a non-significant tendency towards an association between melanoma ...	BeFree	22621339	Detail
<0.001	VITILIGO-ASSOCIATED MULTIPLE AUTOIMMUNE DISEASE SUSCEPTIBILITY 1 (finding)	Carriage of the G allele was higher in vitiligo patients [P = 0.17, OR (95% CI) ...	BeFree	12859622	Detail
0.126	vitiligo	Carriage of the G allele was higher in vitiligo patients [P = 0.17, OR (95% CI) ...	BeFree	12859622	Detail
<0.001	Lentigo	Effect of Val92Met and Arg163Gln variants of the MC1R gene on freckles and solar...	BeFree	17371441	Detail
0.005	Experimental Organism Basal Cell Carcinoma	The melanocyte stimulating hormone receptor polymorphism: association of the V92...	BeFree	10340440	Detail

Annotation

Descrption	Source	Links
NM_002386.4(MC1R):c.274G>A (p.Val92Met) AND Skin/hair/eye pigmentation 2, red hair/fair skin	ClinVar	Detail
NM_002386.4(MC1R):c.274G>A (p.Val92Met) AND Skin/hair/eye pigmentation 2, blond hair/fair skin	ClinVar	Detail
NM_002386.4(MC1R):c.274G>A (p.Val92Met) AND not specified	ClinVar	Detail
NM_002386.4(MC1R):c.274G>A (p.Val92Met) AND Melanoma, cutaneous malignant, susceptibility to, 5	ClinVar	Detail
NM_002386.4(MC1R):c.274G>A (p.Val92Met) AND not provided	ClinVar	Detail
Furthermore, a non-significant tendency towards an association between melanoma risk and MC1R varian...	DisGeNET	Detail
Carriage of the G allele was higher in vitiligo patients [P = 0.17, OR (95% CI) = 1.50 (0.83-2.72)],...	DisGeNET	Detail
Carriage of the G allele was higher in vitiligo patients [P = 0.17, OR (95% CI) = 1.50 (0.83-2.72)],...	DisGeNET	Detail
Effect of Val92Met and Arg163Gln variants of the MC1R gene on freckles and solar lentigines in Japan...	DisGeNET	Detail
The melanocyte stimulating hormone receptor polymorphism: association of the V92M and A294H alleles ...	DisGeNET	Detail

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

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs2228479 dbSNP
Genome: hg38
Position: chr16:89,919,532-89,919,532
Variant Type: snv
Reference Allele: G
Alternative Allele: A
Filtering Status (HGVD): PASS
# of samples (HGVD): 1207
Mean of sample read depth (HGVD): 278.46
Standard deviation of sample read depth (HGVD): 154.47
Number of reference allele (HGVD): 2158
Number of alternative allele (HGVD): 256
Allele Frequency (HGVD): 0.1060480530240265
Gene Symbol (HGVD): MC1R
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)): rs2228479
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.0952
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 1596
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16756
East Asian Chromosome Counts (ExAC): 8536
East Asian Allele Counts (ExAC): 2315
East Asian Heterozygous Counts (ExAC): 1641
East Asian Homozygous Counts (ExAC): 337
East Asian Allele Frequency (ExAC): 0.2712043111527648
Chromosome Counts in All Race (ExAC): 119838
Allele Counts in All Race (ExAC): 9152
Heterozygous Counts in All Race (ExAC): 7984
Homozygous Counts in All Race (ExAC): 584
Allele Frequency in All Race (ExAC): 0.07636976585056493

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