10-31806321-T-G

Position:

• chr10-31806321-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_018287.7(ARHGAP12):​c.*1337A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,512 control chromosomes in the GnomAD database, including 4,730 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 0.24 (4718 hom., cov: 32)
  • Exomes 𝑓: 0.24 (12 hom.)
• Consequence: ARHGAP12 NM_018287.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.55

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]

ARHGAP12 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP12	NM_018287.7	c.*1337A>C		3_prime_UTR_variant	20/20	ENST00000344936.7	NP_060757.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP12	ENST00000344936	c.*1337A>C		3_prime_UTR_variant	20/20	1	NM_018287.7	ENSP00000345808.2

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36440 AN: 151982 Hom.: 4712 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.233

GnomAD4 exome AF: 0.238 AC: 98 AN: 412 Hom.: 12 Cov.: 0 AF XY: 0.254 AC XY: 63 AN XY: 248

Gnomad4 FIN exome AF: 0.239

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.240 AC: 36465 AN: 152100 Hom.: 4718 Cov.: 32 AF XY: 0.243 AC XY: 18040 AN XY: 74354

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.230

Alfa AF: 0.200 Hom.: 5396

Bravo AF: 0.243

Asia WGS AF: 0.310 AC: 1075 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.90

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: rs1044795; hg19: chr10-32095249;