rs3815951

Variant names:

• chr16-24943402-A-G
• rs3815951
• NM_001006634.3:c.1333+369T>C

Variant summary

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

The NM_001006634.3(ARHGAP17):​c.1333+369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,040 control chromosomes in the GnomAD database, including 8,342 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 0.31 (8342 hom., cov: 32)
• Consequence: ARHGAP17 NM_001006634.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 8 publications found

Genes affected

ARHGAP17 (HGNC:18239): (Rho GTPase activating protein 17) RICH1 is a GTPase-activating protein (GAP). GAPs stimulate the intrinsic GTP hydrolysis of small G proteins, such as RHOA (MIM 165390), RAC1 (MIM 602048), and CDC42 (MIM 116952).[supplied by OMIM, Apr 2004]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001006634.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP17	NM_001006634.3	MANE Select	c.1333+369T>C		intron	N/A	NP_001006635.1	Q68EM7-1
	ARHGAP17	NM_018054.6		c.1333+369T>C		intron	N/A	NP_060524.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP17	ENST00000289968.11	TSL:1 MANE Select	c.1333+369T>C		intron	N/A	ENSP00000289968.6	Q68EM7-1
	ARHGAP17	ENST00000303665.9	TSL:1	c.1333+369T>C		intron	N/A	ENSP00000303130.5	Q68EM7-2
	ARHGAP17	ENST00000886927.1		c.1429+369T>C		intron	N/A	ENSP00000556986.1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47155 AN: 151922 Hom.: 8345 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.310 AC: 47152 AN: 152040 Hom.: 8342 Cov.: 32 AF XY: 0.303 AC XY: 22559 AN XY: 74334

African (AFR) AF: 0.166 AC: 6898 AN: 41472

American (AMR) AF: 0.273 AC: 4164 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3468

East Asian (EAS) AF: 0.0923 AC: 478 AN: 5178

South Asian (SAS) AF: 0.238 AC: 1151 AN: 4828

European-Finnish (FIN) AF: 0.351 AC: 3699 AN: 10546

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28257 AN: 67956

Other (OTH) AF: 0.315 AC: 663 AN: 2106

Alfa AF: 0.374 Hom.: 39916

Bravo AF: 0.298

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.28
DANN	Benign	0.80
PhyloP100		-1.3
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: rs3815951; hg19: chr16-24954723;