rs1612554

Variant names:

• chr4-35967126-C-A
• rs1612554
• ENST00000503225.5:n.1741+697G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000503225.5(ARAP2):​n.1741+697G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0857 in 152,084 control chromosomes in the GnomAD database, including 681 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 0.086 (681 hom., cov: 32)
• Consequence: ARAP2 ENST00000503225.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 1 publications found

Genes affected

ARAP2 (HGNC:16924): (ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2) The protein encoded by this gene contains ARF-GAP, RHO-GAP, ankyrin repeat, RAS-associating, and pleckstrin homology domains. The protein is a phosphatidylinositol (3,4,5)-trisphosphate-dependent Arf6 GAP that binds RhoA-GTP, but it lacks the predicted catalytic arginine in the RHO-GAP domain and does not have RHO-GAP activity. The protein associates with focal adhesions and functions downstream of RhoA to regulate focal adhesion dynamics. [provided by RefSeq, Sep 2008]

LOC105374397 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374397	XR_925191.3	n.306+697G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARAP2	ENST00000503225.5	n.1741+697G>T		intron_variant	Intron 12 of 12	1

Frequencies

GnomAD3 genomes AF: 0.0855 AC: 12992 AN: 151966 Hom.: 669 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.0667

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.0561

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.0344

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0857 AC: 13036 AN: 152084 Hom.: 681 Cov.: 32 AF XY: 0.0836 AC XY: 6220 AN XY: 74366

African (AFR) AF: 0.133 AC: 5525 AN: 41468

American (AMR) AF: 0.0666 AC: 1018 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3470

East Asian (EAS) AF: 0.0554 AC: 287 AN: 5178

South Asian (SAS) AF: 0.0496 AC: 239 AN: 4820

European-Finnish (FIN) AF: 0.0344 AC: 364 AN: 10578

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0766 AC: 5205 AN: 67980

Other (OTH) AF: 0.0971 AC: 205 AN: 2112

Alfa AF: 0.0808 Hom.: 284

Bravo AF: 0.0899

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1612554; hg19: chr4-35968748;