rs2970332
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012250.6(RRAS2):c.108+19874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 151,796 control chromosomes in the GnomAD database, including 36,578 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.69 ( 36578 hom., cov: 29)
Consequence
RRAS2
NM_012250.6 intron
NM_012250.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.605
Genes affected
RRAS2 (HGNC:17271): (RAS related 2) This gene encodes a member of the R-Ras subfamily of Ras-like small GTPases. The encoded protein associates with the plasma membrane and may function as a signal transducer. This protein may play an important role in activating signal transduction pathways that control cell proliferation. Mutations in this gene are associated with the growth of certain tumors. Pseudogenes of this gene are found on chromosomes 1 and 2. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.05).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.686 AC: 104007AN: 151678Hom.: 36561 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
104007
AN:
151678
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.686 AC: 104066AN: 151796Hom.: 36578 Cov.: 29 AF XY: 0.682 AC XY: 50560AN XY: 74156 show subpopulations
GnomAD4 genome
AF:
AC:
104066
AN:
151796
Hom.:
Cov.:
29
AF XY:
AC XY:
50560
AN XY:
74156
Gnomad4 AFR
AF:
AC:
0.516602
AN:
0.516602
Gnomad4 AMR
AF:
AC:
0.73677
AN:
0.73677
Gnomad4 ASJ
AF:
AC:
0.813256
AN:
0.813256
Gnomad4 EAS
AF:
AC:
0.592564
AN:
0.592564
Gnomad4 SAS
AF:
AC:
0.765133
AN:
0.765133
Gnomad4 FIN
AF:
AC:
0.667969
AN:
0.667969
Gnomad4 NFE
AF:
AC:
0.771106
AN:
0.771106
Gnomad4 OTH
AF:
AC:
0.708452
AN:
0.708452
Heterozygous variant carriers
0
1542
3085
4627
6170
7712
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
812
1624
2436
3248
4060
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2382
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at