14-61015916-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153811.3(SLC38A6):c.323A>T(p.Tyr108Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000198 in 1,608,276 control chromosomes in the GnomAD database, including 1 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y108C) has been classified as Uncertain significance.
Frequency
Consequence
NM_153811.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC38A6 | NM_153811.3 | c.323A>T | p.Tyr108Phe | missense_variant | 4/16 | ENST00000267488.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC38A6 | ENST00000267488.9 | c.323A>T | p.Tyr108Phe | missense_variant | 4/16 | 1 | NM_153811.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000328 AC: 50AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000602 AC: 148AN: 246030Hom.: 1 AF XY: 0.000557 AC XY: 74AN XY: 132932
GnomAD4 exome AF: 0.000185 AC: 269AN: 1455942Hom.: 1 Cov.: 29 AF XY: 0.000186 AC XY: 135AN XY: 724136
GnomAD4 genome ? AF: 0.000328 AC: 50AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74492
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at