chr15-84905644-C-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_004213.5(SLC28A1):c.709C>A(p.Gln237Lys) variant causes a missense change. The variant allele was found at a frequency of 0.25 in 1,608,760 control chromosomes in the GnomAD database, including 53,745 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_004213.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC28A1 | ENST00000394573.6 | c.709C>A | p.Gln237Lys | missense_variant | 8/19 | 1 | NM_004213.5 | ENSP00000378074.1 | ||
SLC28A1 | ENST00000286749.3 | c.709C>A | p.Gln237Lys | missense_variant | 7/18 | 1 | ENSP00000286749.3 | |||
SLC28A1 | ENST00000538177.5 | c.709C>A | p.Gln237Lys | missense_variant | 7/15 | 2 | ENSP00000443752.1 |
Frequencies
GnomAD3 genomes AF: 0.230 AC: 34972AN: 151980Hom.: 4345 Cov.: 33
GnomAD3 exomes AF: 0.281 AC: 70544AN: 251152Hom.: 11327 AF XY: 0.281 AC XY: 38166AN XY: 135738
GnomAD4 exome AF: 0.252 AC: 366592AN: 1456662Hom.: 49387 Cov.: 31 AF XY: 0.256 AC XY: 185300AN XY: 724882
GnomAD4 genome AF: 0.230 AC: 35018AN: 152098Hom.: 4358 Cov.: 33 AF XY: 0.235 AC XY: 17455AN XY: 74354
ClinVar
Submissions by phenotype
SLC28A1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 01, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at