GeneBe

chr11-14294372-ATT-A

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_012250.6(RRAS2):​c.408+97_408+98delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000483 in 413,878 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: not found (cov: 0)
Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

RRAS2
NM_012250.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.148

Publications

0 publications found
Variant links:
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]
RRAS2 Gene-Disease associations (from GenCC):
  • Noonan syndrome
    Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
  • noonan syndrome 12
    Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics, Genomics England PanelApp
  • ovarian cancer
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RRAS2NM_012250.6 linkc.408+97_408+98delAA intron_variant Intron 4 of 5 ENST00000256196.9 NP_036382.2 P62070-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RRAS2ENST00000256196.9 linkc.408+97_408+98delAA intron_variant Intron 4 of 5 1 NM_012250.6 ENSP00000256196.4 P62070-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000483
AC:
2
AN:
413878
Hom.:
0
AF XY:
0.00000471
AC XY:
1
AN XY:
212256
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
10738
American (AMR)
AF:
0.00
AC:
0
AN:
9952
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
9676
East Asian (EAS)
AF:
0.00
AC:
0
AN:
21280
South Asian (SAS)
AF:
0.00
AC:
0
AN:
24478
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
30782
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1520
European-Non Finnish (NFE)
AF:
0.00000702
AC:
2
AN:
284708
Other (OTH)
AF:
0.00
AC:
0
AN:
20744
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.600
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.15

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

Other links and lift over

dbSNP: rs5789833; hg19: chr11-14315918; API