chr16:89985940:G>A Detail (hg19) (MC1R)

Information

Genome

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

HGVS

Type Transcript Protein
RefSeq NM_002386.3:c.274G>A NP_002377.4:p.Val92Met
Ensemble ENST00000555147.2:c.274G>A ENST00000555147.2:p.Val92Met
ENST00000555427.1:c.274G>A ENST00000555427.1:p.Val92Met
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.106
ToMMo:0.095
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.271

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
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

Annotations

DescrptionSourceLinks
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

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
rs2228479 dbSNP
Genome
hg19
Position
chr16:89,985,940-89,985,940
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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