7-22208909-T-G

Variant names:

• chr7-22208909-T-G
• rs1345251
• NM_012294.5:c.996+10957A>C

Variant summary

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

The NM_012294.5(RAPGEF5):​c.996+10957A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 152,238 control chromosomes in the GnomAD database, including 64,834 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 0.92 (64834 hom., cov: 32)
• Consequence: RAPGEF5 NM_012294.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 3 publications found

Genes affected

RAPGEF5 (HGNC:16862): (Rap guanine nucleotide exchange factor 5) Members of the RAS (see HRAS; MIM 190020) subfamily of GTPases function in signal transduction as GTP/GDP-regulated switches that cycle between inactive GDP- and active GTP-bound states. Guanine nucleotide exchange factors (GEFs), such as RAPGEF5, serve as RAS activators by promoting acquisition of GTP to maintain the active GTP-bound state and are the key link between cell surface receptors and RAS activation (Rebhun et al., 2000 [PubMed 10934204]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAPGEF5	NM_012294.5	c.996+10957A>C		intron_variant	Intron 9 of 25	ENST00000665637.1	NP_036426.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAPGEF5	ENST00000665637.1	c.996+10957A>C		intron_variant	Intron 9 of 25		NM_012294.5	ENSP00000499535.1

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140336 AN: 152120 Hom.: 64780 Cov.: 32

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.923 AC: 140449 AN: 152238 Hom.: 64834 Cov.: 32 AF XY: 0.922 AC XY: 68628 AN XY: 74430

African (AFR) AF: 0.943 AC: 39196 AN: 41554

American (AMR) AF: 0.934 AC: 14290 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3067 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5147 AN: 5180

South Asian (SAS) AF: 0.958 AC: 4616 AN: 4818

European-Finnish (FIN) AF: 0.873 AC: 9242 AN: 10584

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61970 AN: 68020

Other (OTH) AF: 0.918 AC: 1941 AN: 2114

Alfa AF: 0.919 Hom.: 30569

Bravo AF: 0.928

Asia WGS AF: 0.980 AC: 3407 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.69
PhyloP100		0.049
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: rs1345251; hg19: chr7-22248527;