8-1837098-A-G

Variant names:

• chr8-1837098-A-G
• rs4875952
• NM_014629.4:c.-47-6255A>G

Variant summary

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

The NM_001438091.1(ARHGEF10):​c.-47-6255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,194 control chromosomes in the GnomAD database, including 22,729 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 0.54 (22729 hom., cov: 34)
• Consequence: ARHGEF10 NM_001438091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• autosomal dominant slowed nerve conduction velocity

  Inheritance: Unknown, AD Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet
• hereditary peripheral neuropathy

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• peripheral neuropathy

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

KBTBD11-OT1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001438091.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGEF10	NM_014629.4	MANE Select	c.-47-6255A>G		intron	N/A	NP_055444.2
	ARHGEF10	NM_001438091.1		c.-47-6255A>G		intron	N/A	NP_001425020.1
	ARHGEF10	NM_001308153.3		c.-47-6255A>G		intron	N/A	NP_001295082.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGEF10	ENST00000349830.8	TSL:1 MANE Select	c.-47-6255A>G		intron	N/A	ENSP00000340297.3
	ARHGEF10	ENST00000518288.5	TSL:1	c.26-6255A>G		intron	N/A	ENSP00000431012.1
	ARHGEF10	ENST00000520359.5	TSL:1	c.-47-6255A>G		intron	N/A	ENSP00000427909.1

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82382 AN: 152074 Hom.: 22694 Cov.: 34

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.542 AC: 82476 AN: 152194 Hom.: 22729 Cov.: 34 AF XY: 0.550 AC XY: 40954 AN XY: 74398

African (AFR) AF: 0.468 AC: 19425 AN: 41522

American (AMR) AF: 0.623 AC: 9522 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3617 AN: 5178

South Asian (SAS) AF: 0.679 AC: 3277 AN: 4826

European-Finnish (FIN) AF: 0.581 AC: 6150 AN: 10584

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37089 AN: 68000

Other (OTH) AF: 0.482 AC: 1020 AN: 2114

Alfa AF: 0.541 Hom.: 37282

Bravo AF: 0.539

Asia WGS AF: 0.679 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-0.041
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: rs4875952; hg19: chr8-1785264;