3-141487086-G-GGCGGCGGCGGCGCCTGCTGCTGCGGCGGCGGCGCCTGCTGCT
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PM4
The NM_006506.5(RASA2):c.32_33insGGCGCCTGCTGCTGCGGCGGCGGCGCCTGCTGCTGCGGCGGC(p.Ala11_Ser12insAlaProAlaAlaAlaAlaAlaAlaProAlaAlaAlaAlaAla) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000829 in 1,206,558 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006506.5 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASA2 | NM_006506.5 | c.32_33insGGCGCCTGCTGCTGCGGCGGCGGCGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insAlaProAlaAlaAlaAlaAlaAlaProAlaAlaAlaAlaAla | inframe_insertion | 1/24 | ENST00000286364.9 | |
RASA2 | NM_001303245.3 | c.32_33insGGCGCCTGCTGCTGCGGCGGCGGCGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insAlaProAlaAlaAlaAlaAlaAlaProAlaAlaAlaAlaAla | inframe_insertion | 1/24 | ||
RASA2 | NM_001303246.3 | c.32_33insGGCGCCTGCTGCTGCGGCGGCGGCGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insAlaProAlaAlaAlaAlaAlaAlaProAlaAlaAlaAlaAla | inframe_insertion | 1/25 | ||
RASA2 | XM_047448652.1 | c.32_33insGGCGCCTGCTGCTGCGGCGGCGGCGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insAlaProAlaAlaAlaAlaAlaAlaProAlaAlaAlaAlaAla | inframe_insertion | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASA2 | ENST00000286364.9 | c.32_33insGGCGCCTGCTGCTGCGGCGGCGGCGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insAlaProAlaAlaAlaAlaAlaAlaProAlaAlaAlaAlaAla | inframe_insertion | 1/24 | 1 | NM_006506.5 | P1 | |
RASA2 | ENST00000515549.1 | c.32_33insGGCGCCTGCTGCTGCGGCGGCGGCGCCTGCTGCTGCGGCGGC | p.Ala11_Ser12insAlaProAlaAlaAlaAlaAlaAlaProAlaAlaAlaAlaAla | inframe_insertion, NMD_transcript_variant | 1/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 150376Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome AF: 8.29e-7 AC: 1AN: 1206558Hom.: 0 Cov.: 31 AF XY: 0.00000169 AC XY: 1AN XY: 591788
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000665 AC: 1AN: 150376Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73410
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 26, 2022 | This variant is not present in population databases (gnomAD no frequency). This variant, c.32_33ins42, results in the insertion of 14 amino acid(s) of the RASA2 protein (p.Ala11_Ser12ins14), but otherwise preserves the integrity of the reading frame. This variant has not been reported in the literature in individuals affected with RASA2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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
Publications
No publications associated with this variant yet.