rs281875187
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_003070.5(SMARCA2):c.3476G>A(p.Arg1159Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1159L) has been classified as Pathogenic.
Frequency
Consequence
NM_003070.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA2 | NM_003070.5 | c.3476G>A | p.Arg1159Gln | missense_variant | 25/34 | ENST00000349721.8 | |
SMARCA2 | NM_001289396.1 | c.3476G>A | p.Arg1159Gln | missense_variant | 25/34 | ||
SMARCA2 | NM_139045.4 | c.3476G>A | p.Arg1159Gln | missense_variant | 25/33 | ||
SMARCA2 | NM_001289397.2 | c.3302G>A | p.Arg1101Gln | missense_variant | 25/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA2 | ENST00000349721.8 | c.3476G>A | p.Arg1159Gln | missense_variant | 25/34 | 5 | NM_003070.5 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Nicolaides-Baraitser syndrome Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jan 01, 2019 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 26, 2012 | - - |
not provided Pathogenic:1Other:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 24, 2020 | - - |
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
SMARCA2-related BAFopathy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jun 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at