chr2-143671039-C-G

Variant names:

• chr2-143671039-C-G
• rs10928195
• NM_018460.4:c.1139-32380C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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:40949): (ARHGAP15 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018460.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP15	NM_018460.4	MANE Select	c.1139-32380C>G		intron	N/A	NP_060930.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP15	ENST00000295095.11	TSL:1 MANE Select	c.1139-32380C>G		intron	N/A	ENSP00000295095.6
	ARHGAP15	ENST00000906468.1		c.1220-32380C>G		intron	N/A	ENSP00000576527.1
	ARHGAP15	ENST00000906471.1		c.1139-32380C>G		intron	N/A	ENSP00000576530.1

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

African (AFR) AF: 0.602 AC: 24961 AN: 41436

American (AMR) AF: 0.797 AC: 12171 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3005 AN: 3472

East Asian (EAS) AF: 0.920 AC: 4749 AN: 5162

South Asian (SAS) AF: 0.900 AC: 4343 AN: 4828

European-Finnish (FIN) AF: 0.886 AC: 9399 AN: 10604

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58801 AN: 67992

Other (OTH) AF: 0.805 AC: 1698 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.7
DANN	Benign	0.76
PhyloP100		0.021
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10928195; hg19: chr2-144428608;