rs141499372
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_003764.4(STX11):c.589G>A(p.Val197Met) variant causes a missense change. The variant allele was found at a frequency of 0.000396 in 1,613,968 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V197L) has been classified as Uncertain significance.
Frequency
Consequence
NM_003764.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX11 | NM_003764.4 | c.589G>A | p.Val197Met | missense_variant | 2/2 | ENST00000367568.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX11 | ENST00000367568.5 | c.589G>A | p.Val197Met | missense_variant | 2/2 | 1 | NM_003764.4 | P1 | |
STX11 | ENST00000698355.1 | c.589G>A | p.Val197Met | missense_variant | 3/3 | P1 | |||
STX11 | ENST00000698356.1 | c.589G>A | p.Val197Met | missense_variant | 4/4 | P1 | |||
STX11 | ENST00000698357.1 | c.589G>A | p.Val197Met | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000401 AC: 61AN: 152260Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000479 AC: 120AN: 250760Hom.: 0 AF XY: 0.000678 AC XY: 92AN XY: 135694
GnomAD4 exome AF: 0.000396 AC: 579AN: 1461590Hom.: 1 Cov.: 31 AF XY: 0.000487 AC XY: 354AN XY: 727138
GnomAD4 genome AF: 0.000394 AC: 60AN: 152378Hom.: 1 Cov.: 32 AF XY: 0.000483 AC XY: 36AN XY: 74520
ClinVar
Submissions by phenotype
Familial hemophagocytic lymphohistiocytosis 4 Uncertain:2Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2022 | - - |
Autoinflammatory syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Dec 12, 2016 | - - |
STX11-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 01, 2023 | This variant is classified as likely 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