3-141487095-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_006506.5(RASA2):c.12G>A(p.Ala4Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000016 in 1,378,668 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_006506.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RASA2 | NM_006506.5 | c.12G>A | p.Ala4Ala | synonymous_variant | Exon 1 of 24 | ENST00000286364.9 | NP_006497.2 | |
RASA2 | NM_001303246.3 | c.12G>A | p.Ala4Ala | synonymous_variant | Exon 1 of 25 | NP_001290175.1 | ||
RASA2 | NM_001303245.3 | c.12G>A | p.Ala4Ala | synonymous_variant | Exon 1 of 24 | NP_001290174.1 | ||
RASA2 | XM_047448652.1 | c.12G>A | p.Ala4Ala | synonymous_variant | Exon 1 of 17 | XP_047304608.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASA2 | ENST00000286364.9 | c.12G>A | p.Ala4Ala | synonymous_variant | Exon 1 of 24 | 1 | NM_006506.5 | ENSP00000286364.3 | ||
RASA2 | ENST00000515549.1 | n.12G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 4 | ENSP00000424293.1 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150568Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000296 AC: 2AN: 67558Hom.: 0 AF XY: 0.0000262 AC XY: 1AN XY: 38206
GnomAD4 exome AF: 0.0000163 AC: 20AN: 1228100Hom.: 0 Cov.: 30 AF XY: 0.0000149 AC XY: 9AN XY: 603760
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150568Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73490
ClinVar
Submissions by phenotype
not specified 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. -
RASA2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at