5-81077660-G-A

Variant names:

• chr5-81077660-G-A
• rs10514203
• NM_006909.3:c.888-2461G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006909.3(RASGRF2):​c.888-2461G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,290 control chromosomes in the GnomAD database, including 984 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 0.10 (984 hom., cov: 32)
• Consequence: RASGRF2 NM_006909.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• Publications: 3 publications found

Genes affected

RASGRF2 (HGNC:9876): (Ras protein specific guanine nucleotide releasing factor 2) RAS GTPases cycle between an inactive GDP-bound state and an active GTP-bound state. This gene encodes a calcium-regulated nucleotide exchange factor activating both RAS and RAS-related protein, RAC1, through the exchange of bound GDP for GTP, thereby, coordinating the signaling of distinct mitogen-activated protein kinase pathways. [provided by RefSeq, Oct 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASGRF2	NM_006909.3	c.888-2461G>A		intron_variant	Intron 5 of 26	ENST00000265080.9	NP_008840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASGRF2	ENST00000265080.9	c.888-2461G>A		intron_variant	Intron 5 of 26	1	NM_006909.3	ENSP00000265080.4
RASGRF2	ENST00000503795.1	n.888-2461G>A		intron_variant	Intron 5 of 27	1		ENSP00000421771.1
RASGRF2	ENST00000638442.1	c.888-2461G>A		intron_variant	Intron 5 of 9	5		ENSP00000491428.1
RASGRF2	ENST00000502677.1	n.813-2461G>A		intron_variant	Intron 2 of 6	2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15410 AN: 152172 Hom.: 973 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.102 AC: 15464 AN: 152290 Hom.: 984 Cov.: 32 AF XY: 0.101 AC XY: 7524 AN XY: 74458

African (AFR) AF: 0.176 AC: 7302 AN: 41558

American (AMR) AF: 0.0754 AC: 1153 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0962 AC: 334 AN: 3472

East Asian (EAS) AF: 0.00443 AC: 23 AN: 5188

South Asian (SAS) AF: 0.0863 AC: 417 AN: 4832

European-Finnish (FIN) AF: 0.0913 AC: 968 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0731 AC: 4972 AN: 68016

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0793 Hom.: 981

Bravo AF: 0.105

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.2
DANN	Benign	0.78
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10514203; hg19: chr5-80373479;