rs56027330
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_001098486.2(SLC17A3):c.835G>A(p.Gly279Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,613,334 control chromosomes in the GnomAD database, including 11,020 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001098486.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC17A3 | NM_001098486.2 | c.835G>A | p.Gly279Arg | missense_variant | Exon 8 of 13 | ENST00000397060.8 | NP_001091956.1 | |
SLC17A3 | NM_006632.4 | c.601G>A | p.Gly201Arg | missense_variant | Exon 7 of 12 | NP_006623.2 | ||
LOC124901285 | XR_007059518.1 | n.380-9029C>T | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0898 AC: 13655AN: 152020Hom.: 781 Cov.: 32
GnomAD3 exomes AF: 0.105 AC: 26447AN: 251326Hom.: 1649 AF XY: 0.110 AC XY: 14937AN XY: 135828
GnomAD4 exome AF: 0.115 AC: 167372AN: 1461196Hom.: 10237 Cov.: 33 AF XY: 0.116 AC XY: 84250AN XY: 726938
GnomAD4 genome AF: 0.0898 AC: 13662AN: 152138Hom.: 783 Cov.: 32 AF XY: 0.0908 AC XY: 6749AN XY: 74354
ClinVar
Submissions by phenotype
SLC17A3-related disorder Benign:1
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