NM_006506.5:c.15_32delGCCTGCTGCTGCGGCGGC
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_006506.5(RASA2):c.15_32delGCCTGCTGCTGCGGCGGC(p.Pro6_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 0.00000951 in 1,367,560 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000099 ( 0 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]
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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.15_32delGCCTGCTGCTGCGGCGGC | p.Pro6_Ala11del | disruptive_inframe_deletion | Exon 1 of 24 | ENST00000286364.9 | NP_006497.2 | |
RASA2 | NM_001303246.3 | c.15_32delGCCTGCTGCTGCGGCGGC | p.Pro6_Ala11del | disruptive_inframe_deletion | Exon 1 of 25 | NP_001290175.1 | ||
RASA2 | NM_001303245.3 | c.15_32delGCCTGCTGCTGCGGCGGC | p.Pro6_Ala11del | disruptive_inframe_deletion | Exon 1 of 24 | NP_001290174.1 | ||
RASA2 | XM_047448652.1 | c.15_32delGCCTGCTGCTGCGGCGGC | p.Pro6_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.15_32delGCCTGCTGCTGCGGCGGC | p.Pro6_Ala11del | disruptive_inframe_deletion | Exon 1 of 24 | 1 | NM_006506.5 | ENSP00000286364.3 | ||
RASA2 | ENST00000515549.1 | n.15_32delGCCTGCTGCTGCGGCGGC | non_coding_transcript_exon_variant | Exon 1 of 5 | 4 | ENSP00000424293.1 |
Frequencies
GnomAD3 genomes AF: 0.00000665 AC: 1AN: 150440Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000168 AC: 1AN: 59442Hom.: 0 AF XY: 0.0000300 AC XY: 1AN XY: 33384
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GnomAD4 exome AF: 0.00000986 AC: 12AN: 1217120Hom.: 0 AF XY: 0.0000100 AC XY: 6AN XY: 597624
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GnomAD4 genome AF: 0.00000665 AC: 1AN: 150440Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73430
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at