chrX-129465529-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001282874.2(SMARCA1):c.3021G>T(p.Arg1007Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R1007R) has been classified as Likely benign.
Frequency
Consequence
NM_001282874.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA1 | ENST00000371121.5 | c.3021G>T | p.Arg1007Ser | missense_variant | Exon 23 of 25 | 1 | NM_001282874.2 | ENSP00000360162.4 | ||
SMARCA1 | ENST00000371123.5 | c.2985G>T | p.Arg995Ser | missense_variant | Exon 22 of 24 | 1 | ENSP00000360164.2 | |||
SMARCA1 | ENST00000371122.8 | c.3021G>T | p.Arg1007Ser | missense_variant | Exon 23 of 25 | 1 | ENSP00000360163.4 | |||
SMARCA1 | ENST00000617310.4 | n.3339G>T | non_coding_transcript_exon_variant | Exon 21 of 23 | 2 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 26
GnomAD4 genome Cov.: 23
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.