rs2970332

chr11-14338889-G-Achr11-14338889-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

ACMG classification

Verdict is Benign. Variant got -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

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RRAS2	NM_012250.6	c.108+19874C>T		intron_variant		ENST00000256196.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RRAS2	ENST00000256196.9	c.108+19874C>T		intron_variant		1	NM_012250.6	P1

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104007 AN: 151678 Hom.: 36561 Cov.: 29

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.706

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.686 AC: 104066 AN: 151796 Hom.: 36578 Cov.: 29 AF XY: 0.682 AC XY: 50560 AN XY: 74156

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.708

Alfa AF: 0.756 Hom.: 36055

Bravo AF: 0.681

Asia WGS AF: 0.685 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.37
Dann	Benign	0.73

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

Other links and lift over

dbSNP: rs2970332; hg19: chr11-14360435;