rs770885495
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_003070.5(SMARCA2):c.3192G>A(p.Ala1064=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000889 in 1,461,800 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. A1064A) has been classified as Likely benign.
Frequency
Consequence
NM_003070.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA2 | NM_003070.5 | c.3192G>A | p.Ala1064= | synonymous_variant | 23/34 | ENST00000349721.8 | |
SMARCA2 | NM_001289396.1 | c.3192G>A | p.Ala1064= | synonymous_variant | 23/34 | ||
SMARCA2 | NM_139045.4 | c.3192G>A | p.Ala1064= | synonymous_variant | 23/33 | ||
SMARCA2 | NM_001289397.2 | c.3018G>A | p.Ala1006= | synonymous_variant | 23/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA2 | ENST00000349721.8 | c.3192G>A | p.Ala1064= | synonymous_variant | 23/34 | 5 | NM_003070.5 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251448Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135894
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461800Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727212
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 30, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | SMARCA2: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at