rs62622817
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PVS1_ModerateBP6_Very_StrongBS2
The NM_003079.5(SMARCE1):c.1231G>T(p.Glu411Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.000771 in 1,612,022 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. E411E) has been classified as Uncertain significance.
Frequency
Consequence
NM_003079.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCE1 | NM_003079.5 | c.1231G>T | p.Glu411Ter | stop_gained | 11/11 | ENST00000348513.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCE1 | ENST00000348513.12 | c.1231G>T | p.Glu411Ter | stop_gained | 11/11 | 1 | NM_003079.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00415 AC: 631AN: 152166Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00116 AC: 290AN: 250654Hom.: 4 AF XY: 0.000915 AC XY: 124AN XY: 135490
GnomAD4 exome AF: 0.000419 AC: 612AN: 1459738Hom.: 5 Cov.: 29 AF XY: 0.000369 AC XY: 268AN XY: 726294
GnomAD4 genome ? AF: 0.00414 AC: 631AN: 152284Hom.: 1 Cov.: 32 AF XY: 0.00411 AC XY: 306AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | SMARCE1: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 15, 2019 | This variant is associated with the following publications: (PMID: 27149204, 23198860) - |
Rhabdoid tumor predisposition syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Familial meningioma Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2018 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at