rs8327

chr17-45395141-A-G

Variant summary

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

The NM_001282290.2(ARHGAP27):c.*315T>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 0.257 in 413,192 control chromosomes in the GnomAD database, including 15,069 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 0.23 (4464 hom., cov: 32)
  • Exomes 𝑓: 0.27 (10605 hom.)
• Consequence: ARHGAP27 NM_001282290.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

Genes affected

ARHGAP27 (HGNC:31813): (Rho GTPase activating protein 27) This gene encodes a member of a large family of proteins that activate Rho-type guanosine triphosphate (GTP) metabolizing enzymes. The encoded protein may pay a role in clathrin-mediated endocytosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP27	NM_001282290.2	c.*315T>C		3_prime_UTR_variant	20/20	ENST00000685559.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP27	ENST00000685559.1	c.*315T>C		3_prime_UTR_variant	20/20		NM_001282290.2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34520 AN: 151894 Hom.: 4466 Cov.: 32

Gnomad AFR AF: 0.0953

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.237

GnomAD4 exome AF: 0.275 AC: 71716 AN: 261180 Hom.: 10605 Cov.: 2 AF XY: 0.276 AC XY: 37602 AN XY: 136126

Gnomad4 AFR exome AF: 0.0947

Gnomad4 AMR exome AF: 0.201

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.377

Gnomad4 SAS exome AF: 0.289

Gnomad4 FIN exome AF: 0.353

Gnomad4 NFE exome AF: 0.268

Gnomad4 OTH exome AF: 0.264

GnomAD4 genome AF: 0.227 AC: 34531 AN: 152012 Hom.: 4464 Cov.: 32 AF XY: 0.234 AC XY: 17348 AN XY: 74270

Gnomad4 AFR AF: 0.0956

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.237

Alfa AF: 0.264 Hom.: 6898

Bravo AF: 0.211

Asia WGS AF: 0.267 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.3
Dann	Benign	0.29

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: rs8327; hg19: chr17-43472507; COSMIC: COSV65359116; COSMIC: COSV65359116;