rs774483875
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001387283.1(SMARCA4):c.3165C>A(p.Ile1055=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,459,778 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 (★). Synonymous variant affecting the same amino acid position (i.e. I1055I) has been classified as Likely benign.
Frequency
Consequence
NM_001387283.1 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA4 | NM_001387283.1 | c.3165C>A | p.Ile1055= | synonymous_variant | 22/36 | ENST00000646693.2 | |
SMARCA4 | NM_003072.5 | c.3165C>A | p.Ile1055= | synonymous_variant | 22/35 | ENST00000344626.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA4 | ENST00000646693.2 | c.3165C>A | p.Ile1055= | synonymous_variant | 22/36 | NM_001387283.1 | |||
SMARCA4 | ENST00000344626.10 | c.3165C>A | p.Ile1055= | synonymous_variant | 22/35 | 1 | NM_003072.5 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250126Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135482
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1459778Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 726342
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Rhabdoid tumor predisposition syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at