ENST00000409869.5:c.-14-26830C>T

Variant names:

• chr2-143128647-C-T
• rs354706
• ENST00000409869.5:c.-14-26830C>T

Variant summary

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

The ENST00000409869.5(ARHGAP15):​c.-14-26830C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,976 control chromosomes in the GnomAD database, including 20,024 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 0.49 (20024 hom., cov: 32)
• Consequence: ARHGAP15 ENST00000409869.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.36

Genes affected

ARHGAP15 (HGNC:21030): (Rho GTPase activating protein 15) RHO GTPases (see ARHA; MIM 165390) regulate diverse biologic processes, and their activity is regulated by RHO GTPase-activating proteins (GAPs), such as ARHGAP15 (Seoh et al., 2003 [PubMed 12650940]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP15	ENST00000409869.5	c.-14-26830C>T		intron_variant	Intron 2 of 6	5		ENSP00000386560.1

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75159 AN: 151858 Hom.: 20017 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.495 AC: 75197 AN: 151976 Hom.: 20024 Cov.: 32 AF XY: 0.491 AC XY: 36506 AN XY: 74290

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.518

Alfa AF: 0.579 Hom.: 43519

Bravo AF: 0.487

Asia WGS AF: 0.262 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.056
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs354706; hg19: chr2-143886216; COSMIC: COSV54523936; COSMIC: COSV54523936;