X-129448390-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001282874.2(SMARCA1):c.3084G>A(p.Met1028Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000000924 in 1,081,949 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M1028V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001282874.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA1 | ENST00000371121.5 | c.3084G>A | p.Met1028Ile | missense_variant | Exon 24 of 25 | 1 | NM_001282874.2 | ENSP00000360162.4 | ||
SMARCA1 | ENST00000371123.5 | c.3048G>A | p.Met1016Ile | missense_variant | Exon 23 of 24 | 1 | ENSP00000360164.2 | |||
SMARCA1 | ENST00000371122.8 | c.3084G>A | p.Met1028Ile | missense_variant | Exon 24 of 25 | 1 | ENSP00000360163.4 | |||
SMARCA1 | ENST00000617310.4 | n.3402G>A | non_coding_transcript_exon_variant | Exon 22 of 23 | 2 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.00000550 AC: 1AN: 181893Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66549
GnomAD4 exome AF: 9.24e-7 AC: 1AN: 1081949Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 348631
GnomAD4 genome Cov.: 22
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at