3-141487089-G-GGCGGCGGCGCCTGCTGCT
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_006506.5(RASA2):c.15_32dupGCCTGCTGCTGCGGCGGC(p.Ala11_Ser12insProAlaAlaAlaAlaAla) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000497 in 1,367,670 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006506.5 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RASA2 | NM_006506.5 | c.15_32dupGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insProAlaAlaAlaAlaAla | disruptive_inframe_insertion | Exon 1 of 24 | ENST00000286364.9 | NP_006497.2 | |
RASA2 | NM_001303246.3 | c.15_32dupGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insProAlaAlaAlaAlaAla | disruptive_inframe_insertion | Exon 1 of 25 | NP_001290175.1 | ||
RASA2 | NM_001303245.3 | c.15_32dupGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insProAlaAlaAlaAlaAla | disruptive_inframe_insertion | Exon 1 of 24 | NP_001290174.1 | ||
RASA2 | XM_047448652.1 | c.15_32dupGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insProAlaAlaAlaAlaAla | disruptive_inframe_insertion | Exon 1 of 17 | XP_047304608.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASA2 | ENST00000286364.9 | c.15_32dupGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insProAlaAlaAlaAlaAla | disruptive_inframe_insertion | Exon 1 of 24 | 1 | NM_006506.5 | ENSP00000286364.3 | ||
RASA2 | ENST00000515549.1 | n.15_32dupGCCTGCTGCTGCGGCGGC | non_coding_transcript_exon_variant | Exon 1 of 5 | 4 | ENSP00000424293.1 |
Frequencies
GnomAD3 genomes AF: 0.000166 AC: 25AN: 150440Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000168 AC: 1AN: 59442Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 33384
GnomAD4 exome AF: 0.0000353 AC: 43AN: 1217120Hom.: 0 Cov.: 30 AF XY: 0.0000301 AC XY: 18AN XY: 597624
GnomAD4 genome AF: 0.000166 AC: 25AN: 150550Hom.: 0 Cov.: 32 AF XY: 0.000163 AC XY: 12AN XY: 73550
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.15_32dup, results in the insertion of 6 amino acid(s) of the RASA2 protein (p.Pro6_Ala11dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs772613760, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with RASA2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2421860). 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