11-73325436-G-A

Variant names:

• chr11-73325436-G-A
• rs2027760
• NM_014786.4:c.3192+13606G>A

Variant summary

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

The NM_014786.4(ARHGEF17):​c.3192+13606G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,120 control chromosomes in the GnomAD database, including 2,958 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 0.17 (2958 hom., cov: 32)
• Consequence: ARHGEF17 NM_014786.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 13 publications found

Genes affected

ARHGEF17 (HGNC:21726): (Rho guanine nucleotide exchange factor 17) Enables guanyl-nucleotide exchange factor activity. Acts upstream of or within actin cytoskeleton organization. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014786.4. 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
	ARHGEF17	NM_014786.4	MANE Select	c.3192+13606G>A		intron	N/A	NP_055601.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGEF17	ENST00000263674.4	TSL:1 MANE Select	c.3192+13606G>A		intron	N/A	ENSP00000263674.3
	ARHGEF17	ENST00000544519.1	TSL:4	c.264+13606G>A		intron	N/A	ENSP00000441135.1

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25661 AN: 152002 Hom.: 2936 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.169 AC: 25720 AN: 152120 Hom.: 2958 Cov.: 32 AF XY: 0.168 AC XY: 12530 AN XY: 74376

African (AFR) AF: 0.328 AC: 13597 AN: 41456

American (AMR) AF: 0.112 AC: 1707 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3468

East Asian (EAS) AF: 0.0416 AC: 215 AN: 5172

South Asian (SAS) AF: 0.0934 AC: 451 AN: 4828

European-Finnish (FIN) AF: 0.150 AC: 1591 AN: 10598

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7513 AN: 67988

Other (OTH) AF: 0.138 AC: 291 AN: 2110

Alfa AF: 0.154 Hom.: 309

Bravo AF: 0.169

Asia WGS AF: 0.0980 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.0020
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2027760; hg19: chr11-73036481;