rs26907

chr5-81069496-G-Achr5-81069496-G-T

Variant summary

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

The NM_006909.3(RASGRF2):c.544-996G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,194 control chromosomes in the GnomAD database, including 1,912 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 0.15 (1912 hom., cov: 33)
• Consequence: RASGRF2 NM_006909.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RASGRF2	NM_006909.3	c.544-996G>A		intron_variant		ENST00000265080.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RASGRF2	ENST00000265080.9	c.544-996G>A		intron_variant		1	NM_006909.3	P1
RASGRF2	ENST00000503795.1	c.544-996G>A		intron_variant, NMD_transcript_variant		1
RASGRF2	ENST00000638442.1	c.544-996G>A		intron_variant		5
RASGRF2	ENST00000514946.1	n.435-996G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23350 AN: 152076 Hom.: 1913 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.153 AC: 23350 AN: 152194 Hom.: 1912 Cov.: 33 AF XY: 0.155 AC XY: 11525 AN XY: 74430

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.147

Alfa AF: 0.152 Hom.: 3879

Bravo AF: 0.163

Asia WGS AF: 0.119 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	12
Dann	Benign	0.76

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: rs26907; hg19: chr5-80365315;