NM_006506.5:c.12_32delGGCGCCTGCTGCTGCGGCGGC
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_006506.5(RASA2):c.12_32delGGCGCCTGCTGCTGCGGCGGC(p.Ala5_Ala11del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,206,556 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000041 ( 1 hom. )
Consequence
RASA2
NM_006506.5 disruptive_inframe_deletion
NM_006506.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.08
Genes affected
RASA2 (HGNC:9872): (RAS p21 protein activator 2) The protein encoded by this gene is member of the GAP1 family of GTPase-activating proteins. The gene product stimulates the GTPase activity of normal RAS p21 but not its oncogenic counterpart. Acting as a suppressor of RAS function, the protein enhances the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS, thereby allowing control of cellular proliferation and differentiation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_006506.5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RASA2 | NM_006506.5 | c.12_32delGGCGCCTGCTGCTGCGGCGGC | p.Ala5_Ala11del | disruptive_inframe_deletion | Exon 1 of 24 | ENST00000286364.9 | NP_006497.2 | |
RASA2 | NM_001303246.3 | c.12_32delGGCGCCTGCTGCTGCGGCGGC | p.Ala5_Ala11del | disruptive_inframe_deletion | Exon 1 of 25 | NP_001290175.1 | ||
RASA2 | NM_001303245.3 | c.12_32delGGCGCCTGCTGCTGCGGCGGC | p.Ala5_Ala11del | disruptive_inframe_deletion | Exon 1 of 24 | NP_001290174.1 | ||
RASA2 | XM_047448652.1 | c.12_32delGGCGCCTGCTGCTGCGGCGGC | p.Ala5_Ala11del | disruptive_inframe_deletion | Exon 1 of 17 | XP_047304608.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASA2 | ENST00000286364.9 | c.12_32delGGCGCCTGCTGCTGCGGCGGC | p.Ala5_Ala11del | disruptive_inframe_deletion | Exon 1 of 24 | 1 | NM_006506.5 | ENSP00000286364.3 | ||
RASA2 | ENST00000515549.1 | n.12_32delGGCGCCTGCTGCTGCGGCGGC | non_coding_transcript_exon_variant | Exon 1 of 5 | 4 | ENSP00000424293.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000356 AC: 2AN: 56244Hom.: 1 AF XY: 0.0000636 AC XY: 2AN XY: 31426
GnomAD3 exomes
AF:
AC:
2
AN:
56244
Hom.:
AF XY:
AC XY:
2
AN XY:
31426
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000414 AC: 5AN: 1206556Hom.: 1 AF XY: 0.00000676 AC XY: 4AN XY: 591786
GnomAD4 exome
AF:
AC:
5
AN:
1206556
Hom.:
AF XY:
AC XY:
4
AN XY:
591786
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at