rs35646404
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000270570.8(SLC47A1):c.476C>T(p.Thr159Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000383 in 1,614,140 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000270570.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC47A1 | NM_018242.3 | c.476C>T | p.Thr159Met | missense_variant | 5/17 | ENST00000270570.8 | NP_060712.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC47A1 | ENST00000270570.8 | c.476C>T | p.Thr159Met | missense_variant | 5/17 | 1 | NM_018242.3 | ENSP00000270570 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251458Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135906
GnomAD4 exome AF: 0.000406 AC: 593AN: 1461866Hom.: 1 Cov.: 31 AF XY: 0.000377 AC XY: 274AN XY: 727232
GnomAD4 genome AF: 0.000171 AC: 26AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74468
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at