2-143671039-C-G

Position:

• chr2-143671039-C-G

Variant summary

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

The NM_018460.4(ARHGAP15):​c.1139-32380C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,088 control chromosomes in the GnomAD database, including 48,528 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 0.79 (48528 hom., cov: 31)
• Consequence: ARHGAP15 NM_018460.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

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]

ARHGAP15-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP15	NM_018460.4	c.1139-32380C>G		intron_variant		ENST00000295095.11
ARHGAP15-AS1	XR_007087251.1	n.8581-10271G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP15	ENST00000295095.11	c.1139-32380C>G		intron_variant		1	NM_018460.4	P1
ARHGAP15	ENST00000549436.5	n.301-32380C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120080 AN: 151970 Hom.: 48496 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.790 AC: 120157 AN: 152088 Hom.: 48528 Cov.: 31 AF XY: 0.792 AC XY: 58911 AN XY: 74354

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.805

Alfa AF: 0.856 Hom.: 30622

Bravo AF: 0.777

Asia WGS AF: 0.887 AC: 3081 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.7
DANN	Benign	0.76

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: rs10928195; hg19: chr2-144428608;