rs1394181436

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_006506.5(RASA2):​c.14C>A​(p.Ala5Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000163 in 1,230,644 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000016 ( 0 hom. )

Consequence

RASA2
NM_006506.5 missense

Scores

3
1
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.276
Variant links:
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 (MetaRNN=0.18187171).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RASA2NM_006506.5 linkc.14C>A p.Ala5Glu missense_variant Exon 1 of 24 ENST00000286364.9 NP_006497.2 Q15283-2
RASA2NM_001303246.3 linkc.14C>A p.Ala5Glu missense_variant Exon 1 of 25 NP_001290175.1 Q15283
RASA2NM_001303245.3 linkc.14C>A p.Ala5Glu missense_variant Exon 1 of 24 NP_001290174.1 Q15283-1
RASA2XM_047448652.1 linkc.14C>A p.Ala5Glu missense_variant Exon 1 of 17 XP_047304608.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RASA2ENST00000286364.9 linkc.14C>A p.Ala5Glu missense_variant Exon 1 of 24 1 NM_006506.5 ENSP00000286364.3 Q15283-2
RASA2ENST00000515549.1 linkn.14C>A non_coding_transcript_exon_variant Exon 1 of 5 4 ENSP00000424293.1 D6RBA9

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000163
AC:
2
AN:
1230644
Hom.:
0
Cov.:
31
AF XY:
0.00000165
AC XY:
1
AN XY:
605214
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000401
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000101
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
0.0027
T
BayesDel_noAF
Benign
-0.23
CADD
Benign
19
DANN
Benign
0.94
DEOGEN2
Benign
0.23
.;T
Eigen
Benign
-0.52
Eigen_PC
Benign
-0.60
FATHMM_MKL
Benign
0.15
N
LIST_S2
Benign
0.47
T;T
M_CAP
Pathogenic
0.61
D
MetaRNN
Benign
0.18
T;T
MetaSVM
Benign
-0.79
T
MutationAssessor
Benign
0.0
N;.
PrimateAI
Pathogenic
0.83
D
PROVEAN
Benign
-0.13
N;N
REVEL
Benign
0.14
Sift
Pathogenic
0.0
D;D
Sift4G
Uncertain
0.041
D;D
Vest4
0.22
MutPred
0.21
Gain of solvent accessibility (P = 0.0411);Gain of solvent accessibility (P = 0.0411);
MVP
0.74
MPC
0.40
ClinPred
0.61
D
GERP RS
0.69
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.0
gMVP
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1394181436; hg19: chr3-141205939; API