rs40132
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016180.5(SLC45A2):c.1156+956T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 152,150 control chromosomes in the GnomAD database, including 1,253 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.074 ( 1253 hom., cov: 33)
Consequence
SLC45A2
NM_016180.5 intron
NM_016180.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.313
Genes affected
SLC45A2 (HGNC:16472): (solute carrier family 45 member 2) This gene encodes a transporter protein that mediates melanin synthesis. The protein is expressed in a high percentage of melanoma cell lines. Mutations in this gene are a cause of oculocutaneous albinism type 4, and polymorphisms in this gene are associated with variations in skin and hair color. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC45A2 | NM_016180.5 | c.1156+956T>C | intron_variant | ENST00000296589.9 | |||
SLC45A2 | NM_001012509.4 | c.1156+956T>C | intron_variant | ||||
SLC45A2 | XM_047417259.1 | c.916+956T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC45A2 | ENST00000296589.9 | c.1156+956T>C | intron_variant | 1 | NM_016180.5 | P1 | |||
SLC45A2 | ENST00000382102.7 | c.1156+956T>C | intron_variant | 1 | |||||
SLC45A2 | ENST00000510600.1 | c.631+956T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0734 AC: 11152AN: 152032Hom.: 1240 Cov.: 33
GnomAD3 genomes
?
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11152
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152032
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0735 AC: 11187AN: 152150Hom.: 1253 Cov.: 33 AF XY: 0.0811 AC XY: 6032AN XY: 74388
GnomAD4 genome
?
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11187
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152150
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33
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6032
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74388
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830
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at