9-131674641-C-T

Position:

• chr9-131674641-C-T

Variant summary

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

The NM_001377935.1(RAPGEF1):​c.62-23692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,194 control chromosomes in the GnomAD database, including 669 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 0.087 (669 hom., cov: 32)
• Consequence: RAPGEF1 NM_001377935.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

RAPGEF1 (HGNC:4568): (Rap guanine nucleotide exchange factor 1) This gene encodes a human guanine nucleotide exchange factor. It transduces signals from CRK by binding the SH3 domain of CRK, and activating several members of the Ras family of GTPases. This signaling cascade that may be involved in apoptosis, integrin-mediated signal transduction, and cell transformation. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAPGEF1	NM_001377935.1	c.62-23692G>A		intron_variant		ENST00000683357.1	NP_001364864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAPGEF1	ENST00000683357.1	c.62-23692G>A		intron_variant			NM_001377935.1	ENSP00000508246

Frequencies

GnomAD3 genomes AF: 0.0873 AC: 13276 AN: 152076 Hom.: 669 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0873 AC: 13283 AN: 152194 Hom.: 669 Cov.: 32 AF XY: 0.0872 AC XY: 6486 AN XY: 74406

Gnomad4 AFR AF: 0.0939

Gnomad4 AMR AF: 0.0832

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0627

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0834 Hom.: 74

Bravo AF: 0.0893

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.70

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: rs752090; hg19: chr9-134550028;