rs200794965
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1
This summary comes from the ClinGen Evidence Repository: The filtering allele frequency of the c.2156G>C (p.Gly719Ala) variant in the SOS1 gene is 0.0414% (37/66598) of European chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as likely benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BS1; PMID:29493581) LINK:https://erepo.genome.network/evrepo/ui/classification/CA297202/MONDO:0021060/004
Frequency
Consequence
ENST00000402219.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SOS1 | NM_005633.4 | c.2156G>C | p.Gly719Ala | missense_variant | 13/23 | ENST00000402219.8 | NP_005624.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SOS1 | ENST00000402219.8 | c.2156G>C | p.Gly719Ala | missense_variant | 13/23 | 1 | NM_005633.4 | ENSP00000384675 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000396 AC: 6AN: 151686Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000187 AC: 47AN: 250736Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135502
GnomAD4 exome AF: 0.0000902 AC: 131AN: 1452508Hom.: 0 Cov.: 30 AF XY: 0.0000940 AC XY: 68AN XY: 723312
GnomAD4 genome AF: 0.0000396 AC: 6AN: 151686Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74082
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 30, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 01, 2021 | This variant is associated with the following publications: (PMID: 32603605) - |
RASopathy Benign:2
Likely benign, reviewed by expert panel | curation | ClinGen RASopathy Variant Curation Expert Panel | Apr 18, 2017 | The filtering allele frequency of the c.2156G>C (p.Gly719Ala) variant in the SOS1 gene is 0.0414% (37/66598) of European chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as likely benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BS1; PMID:29493581) - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 08, 2024 | - - |
Primary dilated cardiomyopathy Uncertain:1
Uncertain significance, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 09, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Noonan syndrome and Noonan-related syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Nov 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at