rs538827438
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_006506.5(RASA2):c.5C>T(p.Ala2Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000441 in 1,360,180 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 Uncertain significance (★).
Frequency
Consequence
NM_006506.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RASA2 | NM_006506.5 | c.5C>T | p.Ala2Val | missense_variant | Exon 1 of 24 | ENST00000286364.9 | NP_006497.2 | |
RASA2 | NM_001303246.3 | c.5C>T | p.Ala2Val | missense_variant | Exon 1 of 25 | NP_001290175.1 | ||
RASA2 | NM_001303245.3 | c.5C>T | p.Ala2Val | missense_variant | Exon 1 of 24 | NP_001290174.1 | ||
RASA2 | XM_047448652.1 | c.5C>T | p.Ala2Val | missense_variant | Exon 1 of 17 | XP_047304608.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150410Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000174 AC: 1AN: 57574Hom.: 0 AF XY: 0.0000310 AC XY: 1AN XY: 32220
GnomAD4 exome AF: 0.00000331 AC: 4AN: 1209664Hom.: 0 Cov.: 30 AF XY: 0.00000337 AC XY: 2AN XY: 593490
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150516Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73528
ClinVar
Submissions by phenotype
not provided Uncertain:1
ClinVar contains an entry for this variant (Variation ID: 1432016). This variant has not been reported in the literature in individuals affected with RASA2-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2 of the RASA2 protein (p.Ala2Val). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at