8-17538906-G-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 2P and 14B. PM1BP4_StrongBP6_ModerateBA1
The ENST00000004531.14(SLC7A2):āc.82G>Cā(p.Asp28His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,606,984 control chromosomes in the GnomAD database, including 37,478 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
ENST00000004531.14 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC7A2 | NM_001370338.1 | c.-22-4412G>C | intron_variant | ENST00000494857.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC7A2 | ENST00000494857.6 | c.-22-4412G>C | intron_variant | 5 | NM_001370338.1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.225 AC: 34152AN: 151878Hom.: 4075 Cov.: 32
GnomAD3 exomes AF: 0.191 AC: 47619AN: 249004Hom.: 5058 AF XY: 0.188 AC XY: 25390AN XY: 135106
GnomAD4 exome AF: 0.209 AC: 304812AN: 1454988Hom.: 33401 Cov.: 32 AF XY: 0.207 AC XY: 149531AN XY: 724098
GnomAD4 genome AF: 0.225 AC: 34166AN: 151996Hom.: 4077 Cov.: 32 AF XY: 0.220 AC XY: 16365AN XY: 74282
ClinVar
Submissions by phenotype
SLC7A2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 01, 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