rs11995882

Positions:

• chr8-1913805-A-G

Variant summary

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

The NM_014629.4(ARHGEF10):​c.2143+4335A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,196 control chromosomes in the GnomAD database, including 1,761 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 (1761 hom., cov: 33)
• Consequence: ARHGEF10 NM_014629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

Genes affected

ARHGEF10 (HGNC:14103): (Rho guanine nucleotide exchange factor 10) This gene encodes a Rho guanine nucleotide exchange factor (GEF). Rho GEFs regulate the activity of small Rho GTPases by stimulating the exchange of guanine diphosphate (GDP) for guanine triphosphate (GTP) and may play a role in neural morphogenesis. Mutations in this gene are associated with slowed nerve conduction velocity (SNCV). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

ARHGEF10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGEF10	NM_014629.4	c.2143+4335A>G		intron_variant		ENST00000349830.8	NP_055444.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGEF10	ENST00000349830.8	c.2143+4335A>G		intron_variant		1	NM_014629.4	ENSP00000340297.3
KBTBD11-OT1	ENST00000635855.1	n.*2097+4335A>G		intron_variant		5		ENSP00000489726.1

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22394 AN: 152078 Hom.: 1758 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.0694

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.147 AC: 22435 AN: 152196 Hom.: 1761 Cov.: 33 AF XY: 0.146 AC XY: 10853 AN XY: 74404

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.0694

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.146

Alfa AF: 0.149 Hom.: 3715

Bravo AF: 0.144

Asia WGS AF: 0.0550 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.69

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: rs11995882; hg19: chr8-1861971;