chr16:89986154:G>A Detail (hg19) (MC1R)

Information

Genome

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

HGVS

Type Transcript Protein
RefSeq NM_002386.3:c.488G>A NP_002377.4:p.Arg163Gln
Ensemble ENST00000639847.1:c.488G>A ENST00000639847.1:p.Arg163Gln
ENST00000555427.1:c.488G>A ENST00000555427.1:p.Arg163Gln
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.790
ToMMo:0.793
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.644

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 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&lt;0.001) associated with severe HTS. BeFree 26030184 Detail
Annotation

Annotations

DescrptionSourceLinks
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&lt;0.001) associated with severe HTS. 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
rs885479 dbSNP
Genome
hg19
Position
chr16:89,986,154-89,986,154
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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