11-35260905-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The ENST00000278379.9(SLC1A2):c.1714C>T(p.Arg572Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000744 in 1,612,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R572H) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000278379.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC1A2 | NM_004171.4 | c.1714C>T | p.Arg572Cys | missense_variant | 11/11 | ENST00000278379.9 | NP_004162.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC1A2 | ENST00000278379.9 | c.1714C>T | p.Arg572Cys | missense_variant | 11/11 | 1 | NM_004171.4 | ENSP00000278379 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152036Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251440Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135892
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460194Hom.: 0 Cov.: 29 AF XY: 0.0000110 AC XY: 8AN XY: 726520
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152036Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74246
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at