rs773341135
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_003072.5(SMARCA4):c.1554G>A(p.Glu518Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003072.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCA4 | NM_001387283.1 | c.1554G>A | p.Glu518Glu | synonymous_variant | Exon 9 of 36 | ENST00000646693.2 | NP_001374212.1 | |
SMARCA4 | NM_003072.5 | c.1554G>A | p.Glu518Glu | synonymous_variant | Exon 9 of 35 | ENST00000344626.10 | NP_003063.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA4 | ENST00000646693.2 | c.1554G>A | p.Glu518Glu | synonymous_variant | Exon 9 of 36 | NM_001387283.1 | ENSP00000495368.1 | |||
SMARCA4 | ENST00000344626.10 | c.1554G>A | p.Glu518Glu | synonymous_variant | Exon 9 of 35 | 1 | NM_003072.5 | ENSP00000343896.4 | ||
SMARCA4 | ENST00000643549.1 | c.1554G>A | p.Glu518Glu | synonymous_variant | Exon 9 of 35 | ENSP00000493975.1 | ||||
SMARCA4 | ENST00000541122.6 | c.1554G>A | p.Glu518Glu | synonymous_variant | Exon 10 of 35 | 5 | ENSP00000445036.2 | |||
SMARCA4 | ENST00000643296.1 | c.1554G>A | p.Glu518Glu | synonymous_variant | Exon 9 of 34 | ENSP00000496635.1 | ||||
SMARCA4 | ENST00000644737.1 | c.1554G>A | p.Glu518Glu | synonymous_variant | Exon 9 of 34 | ENSP00000495548.1 | ||||
SMARCA4 | ENST00000589677.5 | c.1554G>A | p.Glu518Glu | synonymous_variant | Exon 10 of 35 | 5 | ENSP00000464778.1 | |||
SMARCA4 | ENST00000643995.1 | c.966G>A | p.Glu322Glu | synonymous_variant | Exon 6 of 32 | ENSP00000496004.1 | ||||
SMARCA4 | ENST00000644963.1 | c.198G>A | p.Glu66Glu | synonymous_variant | Exon 2 of 28 | ENSP00000495599.1 | ||||
SMARCA4 | ENST00000644065.1 | c.282G>A | p.Glu94Glu | synonymous_variant | Exon 2 of 27 | ENSP00000493615.1 | ||||
SMARCA4 | ENST00000642350.1 | c.42G>A | p.Glu14Glu | synonymous_variant | Exon 1 of 27 | ENSP00000495355.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250836Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135636
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461678Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727126
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Rhabdoid tumor predisposition syndrome 2 Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at