2-68684134-C-T

Variant summary

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

The ENST00000463483.5(ARHGAP25):n.129+4405C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,002 control chromosomes in the GnomAD database, including 5,794 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 0.26 (5794 hom., cov: 32)
• Consequence: ARHGAP25 ENST00000463483.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

Genes affected

ARHGAP25 (HGNC:28951): (Rho GTPase activating protein 25) ARHGAPs, such as ARHGAP25, encode negative regulators of Rho GTPases (see ARHA; MIM 165390), which are implicated in actin remodeling, cell polarity, and cell migration (Katoh and Katoh, 2004 [PubMed 15254788]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP25	ENST00000463483.5	n.129+4405C>T		intron_variant, non_coding_transcript_variant		2
ARHGAP25	ENST00000481684.5	n.250+4039C>T		intron_variant, non_coding_transcript_variant		3
ARHGAP25	ENST00000491237.5	n.134+4039C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39515 AN: 151884 Hom.: 5781 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.260 AC: 39554 AN: 152002 Hom.: 5794 Cov.: 32 AF XY: 0.265 AC XY: 19676 AN XY: 74300

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.239

Alfa AF: 0.181 Hom.: 4476

Bravo AF: 0.265

Asia WGS AF: 0.314 AC: 1091 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	1.6
Dann	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13423988; hg19: chr2-68911266;