chr2-143415131-A-T

Position:

• chr2-143415131-A-T

Variant summary

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

The NM_018460.4(ARHGAP15):​c.475-20470A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,016 control chromosomes in the GnomAD database, including 49,918 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 0.81 (49918 hom., cov: 30)
• Consequence: ARHGAP15 NM_018460.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP15	NM_018460.4	c.475-20470A>T		intron_variant		ENST00000295095.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP15	ENST00000295095.11	c.475-20470A>T		intron_variant		1	NM_018460.4	P1
	ENST00000546678.1	n.309-109671T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122804 AN: 151898 Hom.: 49879 Cov.: 30

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.808 AC: 122898 AN: 152016 Hom.: 49918 Cov.: 30 AF XY: 0.812 AC XY: 60359 AN XY: 74320

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.820

Alfa AF: 0.803 Hom.: 6091

Bravo AF: 0.812

Asia WGS AF: 0.867 AC: 3017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.67

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: rs2381435; hg19: chr2-144172700;