rs1554623112
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_003070.5(SMARCA2):c.2348C>G(p.Ser783Trp) variant causes a missense, splice region 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. 3/3 splice prediction tools predict no significant impact on normal splicing. 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. S783L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_003070.5 missense, splice_region
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.2348C>G | p.Ser783Trp | missense_variant, splice_region_variant | 15/34 | ENST00000349721.8 | |
SMARCA2 | NM_001289396.1 | c.2348C>G | p.Ser783Trp | missense_variant, splice_region_variant | 15/34 | ||
SMARCA2 | NM_139045.4 | c.2348C>G | p.Ser783Trp | missense_variant, splice_region_variant | 15/33 | ||
SMARCA2 | NM_001289397.2 | c.2348C>G | p.Ser783Trp | missense_variant, splice_region_variant | 15/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA2 | ENST00000349721.8 | c.2348C>G | p.Ser783Trp | missense_variant, splice_region_variant | 15/34 | 5 | NM_003070.5 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Nicolaides-Baraitser syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 02, 2015 | - - |
Intellectual disability Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Diagnostic Laboratory, Strasbourg University Hospital | Sep 10, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at