15-84904200-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004213.5(SLC28A1):c.565G>A(p.Val189Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 1,613,866 control chromosomes in the GnomAD database, including 118,329 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004213.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC28A1 | NM_004213.5 | c.565G>A | p.Val189Ile | missense_variant | 7/19 | ENST00000394573.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC28A1 | ENST00000394573.6 | c.565G>A | p.Val189Ile | missense_variant | 7/19 | 1 | NM_004213.5 | P1 | |
SLC28A1 | ENST00000286749.3 | c.565G>A | p.Val189Ile | missense_variant | 6/18 | 1 | P1 | ||
SLC28A1 | ENST00000538177.5 | c.565G>A | p.Val189Ile | missense_variant | 6/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.339 AC: 51482AN: 151998Hom.: 9354 Cov.: 33
GnomAD3 exomes AF: 0.403 AC: 101384AN: 251380Hom.: 22006 AF XY: 0.404 AC XY: 54898AN XY: 135868
GnomAD4 exome AF: 0.381 AC: 556305AN: 1461750Hom.: 108960 Cov.: 61 AF XY: 0.385 AC XY: 279657AN XY: 727186
GnomAD4 genome ? AF: 0.339 AC: 51522AN: 152116Hom.: 9369 Cov.: 33 AF XY: 0.346 AC XY: 25710AN XY: 74348
ClinVar
Submissions by phenotype
SLC28A1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 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