rs17281188
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_033518.4(SLC38A5):āc.1352T>Cā(p.Met451Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0768 in 1,194,220 control chromosomes in the GnomAD database, including 2,564 homozygotes. There are 30,323 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_033518.4 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 |
---|---|---|---|---|---|---|---|
SLC38A5 | NM_033518.4 | c.1352T>C | p.Met451Thr | missense_variant | 17/17 | ENST00000620913.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC38A5 | ENST00000620913.5 | c.1352T>C | p.Met451Thr | missense_variant | 17/17 | 5 | NM_033518.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0760 AC: 8572AN: 112828Hom.: 277 Cov.: 23 AF XY: 0.0756 AC XY: 2646AN XY: 34986
GnomAD3 exomes AF: 0.0846 AC: 12809AN: 151431Hom.: 449 AF XY: 0.0853 AC XY: 3999AN XY: 46885
GnomAD4 exome AF: 0.0769 AC: 83183AN: 1081340Hom.: 2287 Cov.: 33 AF XY: 0.0784 AC XY: 27678AN XY: 352944
GnomAD4 genome ? AF: 0.0759 AC: 8569AN: 112880Hom.: 277 Cov.: 23 AF XY: 0.0755 AC XY: 2645AN XY: 35048
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at