chr16:89919746:G>A Detail (hg38) (MC1R)

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Information

Genome

Assembly	Position
hg19	chr16:89,986,154-89,986,154 View the variant detail on this assembly version.
hg38	chr16:89,919,746-89,919,746

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	tgv56656376	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
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	2018-06-22	criteria provided, single submitter	not provided	germline	Detail
Benign	2022-04-14	criteria provided, single submitter	Melanoma, cutaneous malignant, susceptibility to, 5,Tyrosinase-positive oculocutaneous albinism,Skin/hair/eye pigmentation, variation in, 2,Increased analgesia from kappa-opioid receptor agonist, female-specific	unknown	Detail
Benign	2022-04-14	criteria provided, single submitter	Melanoma, cutaneous malignant, susceptibility to, 5,Tyrosinase-positive oculocutaneous albinism,Skin/hair/eye pigmentation, variation in, 2,Increased analgesia from kappa-opioid receptor agonist, female-specific	unknown	Detail
Benign	2022-04-14	criteria provided, single submitter	Melanoma, cutaneous malignant, susceptibility to, 5,Tyrosinase-positive oculocutaneous albinism,Skin/hair/eye pigmentation, variation in, 2,Increased analgesia from kappa-opioid receptor agonist, female-specific	unknown	Detail
Benign	2022-04-14	criteria provided, single submitter	Melanoma, cutaneous malignant, susceptibility to, 5,Tyrosinase-positive oculocutaneous albinism,Skin/hair/eye pigmentation, variation in, 2,Increased analgesia from kappa-opioid receptor agonist, female-specific	unknown	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
<0.001	melanoma	We aim to examine the influence of the MC1R variants (RHC: D84E, R151C, R160W; N...	BeFree	24170137	Detail
0.284	melanoma	Furthermore, we observed that a carrier of the founder CDKN2A [p.Leu113Leu;p.Pro...	BeFree	17492760	Detail
<0.001	Lentigo	Effect of Val92Met and Arg163Gln variants of the MC1R gene on freckles and solar...	BeFree	17371441	Detail
0.284	melanoma	Distribution of MC1R variants among melanoma subtypes: p.R163Q is associated wit...	BeFree	23647022	Detail
<0.001	Lentigo maligna melanoma	Distribution of MC1R variants among melanoma subtypes: p.R163Q is associated wit...	BeFree	23647022	Detail
<0.001	Hypotrichosis simplex	MC1R SNP R163Q was also significantly (P<0.001) associated with severe HTS.	BeFree	26030184	Detail

Annotation

Descrption	Source	Links
NM_002386.4(MC1R):c.488G>A (p.Arg163Gln) AND not specified	ClinVar	Detail
NM_002386.4(MC1R):c.488G>A (p.Arg163Gln) AND Melanoma, cutaneous malignant, susceptibility to, 5	ClinVar	Detail
NM_002386.4(MC1R):c.488G>A (p.Arg163Gln) AND not provided	ClinVar	Detail
NM_002386.4(MC1R):c.488G>A (p.Arg163Gln) AND multiple conditions	ClinVar	Detail
NM_002386.4(MC1R):c.488G>A (p.Arg163Gln) AND multiple conditions	ClinVar	Detail
NM_002386.4(MC1R):c.488G>A (p.Arg163Gln) AND multiple conditions	ClinVar	Detail
NM_002386.4(MC1R):c.488G>A (p.Arg163Gln) AND multiple conditions	ClinVar	Detail
We aim to examine the influence of the MC1R variants (RHC: D84E, R151C, R160W; NRHC: V60L, R163Q and...	DisGeNET	Detail
Furthermore, we observed that a carrier of the founder CDKN2A [p.Leu113Leu;p.Pro114Ser] mutation as ...	DisGeNET	Detail
Effect of Val92Met and Arg163Gln variants of the MC1R gene on freckles and solar lentigines in Japan...	DisGeNET	Detail
Distribution of MC1R variants among melanoma subtypes: p.R163Q is associated with lentigo maligna me...	DisGeNET	Detail
Distribution of MC1R variants among melanoma subtypes: p.R163Q is associated with lentigo maligna me...	DisGeNET	Detail
MC1R SNP R163Q was also significantly (P<0.001) associated with severe HTS.	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: rs885479 dbSNP
Genome: hg38
Position: chr16:89,919,746-89,919,746
Variant Type: snv
Reference Allele: G
Alternative Allele: A
Filtering Status (HGVD): PASS
# of samples (HGVD): 1203
Mean of sample read depth (HGVD): 217.94
Standard deviation of sample read depth (HGVD): 107.34
Number of reference allele (HGVD): 506
Number of alternative allele (HGVD): 1900
Allele Frequency (HGVD): 0.7896924355777224
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)): rs885479
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.7926
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 13274
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16748
East Asian Chromosome Counts (ExAC): 8552
East Asian Allele Counts (ExAC): 5509
East Asian Heterozygous Counts (ExAC): 1927
East Asian Homozygous Counts (ExAC): 1791
East Asian Allele Frequency (ExAC): 0.6441768007483629
Chromosome Counts in All Race (ExAC): 119016
Allele Counts in All Race (ExAC): 16166
Heterozygous Counts in All Race (ExAC): 9738
Homozygous Counts in All Race (ExAC): 3214
Allele Frequency in All Race (ExAC): 0.1358304765745782

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