X-129465608-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001282874.2(SMARCA1):c.2942G>A(p.Arg981Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000275 in 1,198,675 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001282874.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA1 | ENST00000371121.5 | c.2942G>A | p.Arg981Lys | missense_variant | Exon 23 of 25 | 1 | NM_001282874.2 | ENSP00000360162.4 | ||
SMARCA1 | ENST00000371123.5 | c.2906G>A | p.Arg969Lys | missense_variant | Exon 22 of 24 | 1 | ENSP00000360164.2 | |||
SMARCA1 | ENST00000371122.8 | c.2942G>A | p.Arg981Lys | missense_variant | Exon 23 of 25 | 1 | ENSP00000360163.4 | |||
SMARCA1 | ENST00000617310.4 | n.3260G>A | non_coding_transcript_exon_variant | Exon 21 of 23 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000625 AC: 7AN: 111995Hom.: 0 Cov.: 22 AF XY: 0.0000585 AC XY: 2AN XY: 34167
GnomAD3 exomes AF: 0.0000386 AC: 7AN: 181388Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66088
GnomAD4 exome AF: 0.0000239 AC: 26AN: 1086624Hom.: 0 Cov.: 27 AF XY: 0.00000852 AC XY: 3AN XY: 352294
GnomAD4 genome AF: 0.0000625 AC: 7AN: 112051Hom.: 0 Cov.: 22 AF XY: 0.0000584 AC XY: 2AN XY: 34233
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2942G>A (p.R981K) alteration is located in exon 23 (coding exon 23) of the SMARCA1 gene. This alteration results from a G to A substitution at nucleotide position 2942, causing the arginine (R) at amino acid position 981 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at