rs2808074

Variant names:

• chr10-31890256-A-C
• rs2808074
• NM_018287.7:c.684+17916T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-31890256-A-C
• chr10-31890256-A-G
• chr10-31890256-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018287.7(ARHGAP12):​c.684+17916T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,948 control chromosomes in the GnomAD database, including 16,385 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 0.46 (16385 hom., cov: 31)
• Consequence: ARHGAP12 NM_018287.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 2 publications found

Genes affected

ARHGAP12 (HGNC:16348): (Rho GTPase activating protein 12) This gene encodes a member of a large family of proteins that activate Rho-type guanosine triphosphate (GTP) metabolizing enzymes. The encoded protein may be involved in suppressing tumor formation by regulating cell invasion and adhesion. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP12	NM_018287.7	c.684+17916T>G		intron_variant	Intron 3 of 19	ENST00000344936.7	NP_060757.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP12	ENST00000344936.7	c.684+17916T>G		intron_variant	Intron 3 of 19	1	NM_018287.7	ENSP00000345808.2

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69876 AN: 151830 Hom.: 16367 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.460 AC: 69945 AN: 151948 Hom.: 16385 Cov.: 31 AF XY: 0.456 AC XY: 33848 AN XY: 74256

African (AFR) AF: 0.395 AC: 16369 AN: 41448

American (AMR) AF: 0.505 AC: 7707 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1743 AN: 3472

East Asian (EAS) AF: 0.400 AC: 2065 AN: 5168

South Asian (SAS) AF: 0.476 AC: 2296 AN: 4820

European-Finnish (FIN) AF: 0.360 AC: 3801 AN: 10548

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34368 AN: 67934

Other (OTH) AF: 0.483 AC: 1020 AN: 2110

Alfa AF: 0.466 Hom.: 2520

Bravo AF: 0.470

Asia WGS AF: 0.465 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.77
PhyloP100		1.7
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: rs2808074; hg19: chr10-32179184;