3-141487078-G-A
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006506.5(RASA2):c.-6G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000212 in 1,337,574 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00031 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 0 hom. )
Consequence
RASA2
NM_006506.5 5_prime_UTR
NM_006506.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.856
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 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RASA2 | NM_006506.5 | c.-6G>A | 5_prime_UTR_variant | Exon 1 of 24 | ENST00000286364.9 | NP_006497.2 | ||
RASA2 | NM_001303246.3 | c.-6G>A | 5_prime_UTR_variant | Exon 1 of 25 | NP_001290175.1 | |||
RASA2 | NM_001303245.3 | c.-6G>A | 5_prime_UTR_variant | Exon 1 of 24 | NP_001290174.1 | |||
RASA2 | XM_047448652.1 | c.-6G>A | 5_prime_UTR_variant | Exon 1 of 17 | XP_047304608.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASA2 | ENST00000286364 | c.-6G>A | 5_prime_UTR_variant | Exon 1 of 24 | 1 | NM_006506.5 | ENSP00000286364.3 | |||
RASA2 | ENST00000515549.1 | n.-6G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 4 | ENSP00000424293.1 | ||||
RASA2 | ENST00000515549.1 | n.-6G>A | 5_prime_UTR_variant | Exon 1 of 5 | 4 | ENSP00000424293.1 |
Frequencies
GnomAD3 genomes AF: 0.000314 AC: 47AN: 149918Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000130 AC: 6AN: 46160Hom.: 0 AF XY: 0.000157 AC XY: 4AN XY: 25542
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GnomAD4 exome AF: 0.000200 AC: 237AN: 1187656Hom.: 0 Cov.: 31 AF XY: 0.000187 AC XY: 109AN XY: 581562
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GnomAD4 genome AF: 0.000314 AC: 47AN: 149918Hom.: 1 Cov.: 32 AF XY: 0.000273 AC XY: 20AN XY: 73156
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Jun 30, 2024
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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Benign
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at