rs190409

chr5-81075502-A-G

Variant summary

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

The NM_006909.3(RASGRF2):c.887+2050A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,920 control chromosomes in the GnomAD database, including 21,914 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 0.53 (21914 hom., cov: 32)
• Consequence: RASGRF2 NM_006909.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RASGRF2	NM_006909.3	c.887+2050A>G		intron_variant		ENST00000265080.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RASGRF2	ENST00000265080.9	c.887+2050A>G		intron_variant		1	NM_006909.3	P1
RASGRF2	ENST00000503795.1	c.887+2050A>G		intron_variant, NMD_transcript_variant		1
RASGRF2	ENST00000638442.1	c.887+2050A>G		intron_variant		5
RASGRF2	ENST00000502677.1	n.812+2050A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80863 AN: 151802 Hom.: 21889 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.533 AC: 80931 AN: 151920 Hom.: 21914 Cov.: 32 AF XY: 0.537 AC XY: 39899 AN XY: 74276

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.486

Alfa AF: 0.543 Hom.: 27377

Bravo AF: 0.522

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.7
Dann	Benign	0.66

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: rs190409; hg19: chr5-80371321;