chr5:33951693:C>G Detail (hg19) (SLC45A2)

Information

Genome

Assembly Position
hg19 chr5:33,951,693-33,951,693
hg38 chr5:33,951,588-33,951,588 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_016180.4:c.1122G>C NP_057264.3:p.Leu374Phe
NM_001012509.3:c.1122G>C NP_001012527.1:p.Leu374Phe
NM_001297417.2:c.*64G>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.002

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606202 OMIM
HGNC 16472 HGNC
Ensembl ENSG00000164175 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv20741143 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2014-12-09 criteria provided, single submitter not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2021-07-15 criteria provided, single submitter Oculocutaneous albinism type 4 germline Detail
Benign 2022-05-24 criteria provided, single submitter Skin/hair/eye pigmentation, variation in, 5,Oculocutaneous albinism type 4 unknown Detail
Benign 2022-05-24 criteria provided, single submitter Skin/hair/eye pigmentation, variation in, 5,Oculocutaneous albinism type 4 unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.122 Skin pigmentation - finding [A genomewide association study of skin pigmentation in a South Asian population... GAD 17999355 Detail
0.005 SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2 (disorder) Three single nucleotide polymorphisms (rs28777, rs35391, and rs16891982) in the ... BeFree 19710684 Detail
<0.001 Experimental Organism Basal Cell Carcinoma A melanoma- and pigmentation-associated variant in the SLC45A2 gene, L374F, is a... BeFree 19578363 Detail
0.122 Skin pigmentation - finding A genomewide association study of skin pigmentation in a South Asian population. GWASCAT 17999355 Detail
0.262 melanoma The correlation of the rs16891982 SNP in the SLC45A2 gene with melanoma was used... BeFree 23786662 Detail
0.123 squamous cell carcinoma A melanoma- and pigmentation-associated variant in the SLC45A2 gene, L374F, is a... BeFree 19578363 Detail
<0.001 SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2 (disorder) Three single nucleotide polymorphisms (rs28777, rs35391, and rs16891982) in the ... BeFree 19710684 Detail
0.262 melanoma A melanoma- and pigmentation-associated variant in the SLC45A2 gene, L374F, is a... BeFree 19578363 Detail
0.033 Albinism, Oculocutaneous The present study analyzed the effects of two human MATP mutations, D93N, which ... BeFree 25760657 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_016180.5(SLC45A2):c.1122G>C (p.Leu374Phe) AND not specified ClinVar Detail
NM_016180.5(SLC45A2):c.1122G>C (p.Leu374Phe) AND not provided ClinVar Detail
NM_016180.5(SLC45A2):c.1122G>C (p.Leu374Phe) AND Oculocutaneous albinism type 4 ClinVar Detail
NM_016180.5(SLC45A2):c.1122G>C (p.Leu374Phe) AND multiple conditions ClinVar Detail
NM_016180.5(SLC45A2):c.1122G>C (p.Leu374Phe) AND multiple conditions ClinVar Detail
[A genomewide association study of skin pigmentation in a South Asian population.] DisGeNET Detail
Three single nucleotide polymorphisms (rs28777, rs35391, and rs16891982) in the MATP gene (SLC45A2) ... DisGeNET Detail
A melanoma- and pigmentation-associated variant in the SLC45A2 gene, L374F, is associated with risk ... DisGeNET Detail
A genomewide association study of skin pigmentation in a South Asian population. DisGeNET Detail
The correlation of the rs16891982 SNP in the SLC45A2 gene with melanoma was used as a case study for... DisGeNET Detail
A melanoma- and pigmentation-associated variant in the SLC45A2 gene, L374F, is associated with risk ... DisGeNET Detail
Three single nucleotide polymorphisms (rs28777, rs35391, and rs16891982) in the MATP gene (SLC45A2) ... DisGeNET Detail
A melanoma- and pigmentation-associated variant in the SLC45A2 gene, L374F, is associated with risk ... DisGeNET Detail
The present study analyzed the effects of two human MATP mutations, D93N, which causes oculocutaneou... 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
rs16891982 dbSNP
Genome
hg19
Position
chr5:33,951,693-33,951,693
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
66.97
Standard deviation of sample read depth (HGVD)
47.21
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
SLC45A2
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))
rs16891982
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8630
East Asian Allele Counts (ExAC)
19
East Asian Heterozygous Counts (ExAC)
17
East Asian Homozygous Counts (ExAC)
1
East Asian Allele Frequency (ExAC)
0.00220162224797219
Chromosome Counts in All Race (ExAC)
121296
Allele Counts in All Race (ExAC)
77666
Heterozygous Counts in All Race (ExAC)
8060
Homozygous Counts in All Race (ExAC)
34803
Allele Frequency in All Race (ExAC)
0.6403014114232951
Genome browser