2-68786119-C-T

Variant names:

• chr2-68786119-C-T
• rs11694785
• NM_001007231.3:c.350-1721C>T

Variant summary

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

The NM_001007231.3(ARHGAP25):​c.350-1721C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,990 control chromosomes in the GnomAD database, including 12,856 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 0.41 (12856 hom., cov: 32)
• Consequence: ARHGAP25 NM_001007231.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP25	NM_001007231.3	c.350-1721C>T		intron_variant	Intron 3 of 10	ENST00000409202.8	NP_001007232.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP25	ENST00000409202.8	c.350-1721C>T		intron_variant	Intron 3 of 10	2	NM_001007231.3	ENSP00000386911.3

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62003 AN: 151872 Hom.: 12851 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.408 AC: 62039 AN: 151990 Hom.: 12856 Cov.: 32 AF XY: 0.408 AC XY: 30326 AN XY: 74302

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.413

Alfa AF: 0.324 Hom.: 1265

Bravo AF: 0.400

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.38

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: rs11694785; hg19: chr2-69013251;