chr16-84009801-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001080442.3(SLC38A8):c.1291G>A(p.Val431Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 1,614,012 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. V431V) has been classified as Likely benign.
Frequency
Consequence
NM_001080442.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC38A8 | NM_001080442.3 | c.1291G>A | p.Val431Ile | missense_variant | 11/11 | ENST00000299709.8 | |
SLC38A8 | XM_017022946.1 | c.1291G>A | p.Val431Ile | missense_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC38A8 | ENST00000299709.8 | c.1291G>A | p.Val431Ile | missense_variant | 11/11 | 5 | NM_001080442.3 | P1 | |
SLC38A8 | ENST00000568003.1 | n.367G>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000874 AC: 133AN: 152220Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000227 AC: 57AN: 251012Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135702
GnomAD4 exome AF: 0.0000869 AC: 127AN: 1461674Hom.: 0 Cov.: 31 AF XY: 0.0000798 AC XY: 58AN XY: 727140
GnomAD4 genome ? AF: 0.000873 AC: 133AN: 152338Hom.: 1 Cov.: 33 AF XY: 0.000779 AC XY: 58AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
SLC38A8-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 07, 2020 | This variant is classified as likely 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