rs3815951

Positions:

• chr16-24943402-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ARHGAP17 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP17	NM_001006634.3	c.1333+369T>C		intron_variant		ENST00000289968.11	NP_001006635.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP17	ENST00000289968.11	c.1333+369T>C		intron_variant		1	NM_001006634.3	ENSP00000289968.6
ARHGAP17	ENST00000303665.9	c.1333+369T>C		intron_variant		1		ENSP00000303130.5
ARHGAP17	ENST00000572314.5	n.3415+369T>C		intron_variant		2
ARHGAP17	ENST00000575412.1	n.72+369T>C		intron_variant		2

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

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.315

Alfa AF: 0.390 Hom.: 25225

Bravo AF: 0.298

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.28
DANN	Benign	0.80

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: rs3815951; hg19: chr16-24954723;