16-25001103-T-A

Position:

• chr16-25001103-T-A

Variant summary

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

The NM_001006634.3(ARHGAP17):​c.53+14106A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,114 control chromosomes in the GnomAD database, including 6,018 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 0.26 (6018 hom., cov: 32)
• Consequence: ARHGAP17 NM_001006634.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP17	NM_001006634.3	c.53+14106A>T		intron_variant		ENST00000289968.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP17	ENST00000289968.11	c.53+14106A>T		intron_variant		1	NM_001006634.3	P3

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39550 AN: 151996 Hom.: 6021 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.260 AC: 39549 AN: 152114 Hom.: 6018 Cov.: 32 AF XY: 0.268 AC XY: 19901 AN XY: 74378

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.259

Alfa AF: 0.286 Hom.: 856

Bravo AF: 0.238

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.83

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: rs10521131; hg19: chr16-25012424;