rs2215054

Variant names:

• chr17-12935692-G-A
• rs2215054
• NM_014859.6:c.583-5364G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-12935692-G-A
• chr17-12935692-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014859.6(ARHGAP44):​c.583-5364G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,070 control chromosomes in the GnomAD database, including 40,006 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 0.72 (40006 hom., cov: 33)
• Consequence: ARHGAP44 NM_014859.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

Genes affected

ARHGAP44 (HGNC:29096): (Rho GTPase activating protein 44) Enables phospholipid binding activity. Predicted to be involved in several processes, including modification of dendritic spine; negative regulation of Rac protein signal transduction; and regulation of plasma membrane bounded cell projection organization. Located in leading edge membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP44	NM_014859.6	c.583-5364G>A		intron_variant	Intron 7 of 20	ENST00000379672.10	NP_055674.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP44	ENST00000379672.10	c.583-5364G>A		intron_variant	Intron 7 of 20	1	NM_014859.6	ENSP00000368994.5

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109990 AN: 151952 Hom.: 39987 Cov.: 33

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.724 AC: 110054 AN: 152070 Hom.: 40006 Cov.: 33 AF XY: 0.726 AC XY: 53973 AN XY: 74330

African (AFR) AF: 0.760 AC: 31503 AN: 41428

American (AMR) AF: 0.768 AC: 11739 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2496 AN: 3470

East Asian (EAS) AF: 0.692 AC: 3578 AN: 5170

South Asian (SAS) AF: 0.755 AC: 3643 AN: 4822

European-Finnish (FIN) AF: 0.719 AC: 7601 AN: 10572

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46897 AN: 68008

Other (OTH) AF: 0.729 AC: 1541 AN: 2114

Alfa AF: 0.704 Hom.: 5716

Bravo AF: 0.730

Asia WGS AF: 0.730 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.66
DANN	Benign	0.43
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2215054; hg19: chr17-12839009;