NM_014859.6:c.1342+252C>T

Variant names:

• chr17-12956998-C-T
• rs7216369
• NM_014859.6:c.1342+252C>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.1342+252C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 152,250 control chromosomes in the GnomAD database, including 534 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.074 (534 hom., cov: 32)
• Consequence: ARHGAP44 NM_014859.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014859.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP44	NM_014859.6	MANE Select	c.1342+252C>T		intron	N/A	NP_055674.4
	ARHGAP44	NM_001321166.2		c.1342+252C>T		intron	N/A	NP_001308095.1	Q17R89-3
	ARHGAP44	NM_001321167.2		c.1342+252C>T		intron	N/A	NP_001308096.1	E7ERK8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP44	ENST00000379672.10	TSL:1 MANE Select	c.1342+252C>T		intron	N/A	ENSP00000368994.5	Q17R89-1
	ARHGAP44	ENST00000340825.7	TSL:1	c.1342+252C>T		intron	N/A	ENSP00000342566.3	Q17R89-3
	ARHGAP44	ENST00000262444.13	TSL:1	c.1342+252C>T		intron	N/A	ENSP00000262444.9	E7ERK8

Frequencies

GnomAD3 genomes AF: 0.0735 AC: 11178 AN: 152132 Hom.: 532 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0736 AC: 11199 AN: 152250 Hom.: 534 Cov.: 32 AF XY: 0.0730 AC XY: 5436 AN XY: 74440

African (AFR) AF: 0.0698 AC: 2899 AN: 41526

American (AMR) AF: 0.0546 AC: 835 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4826

European-Finnish (FIN) AF: 0.0382 AC: 406 AN: 10618

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0773 AC: 5260 AN: 68008

Other (OTH) AF: 0.0823 AC: 174 AN: 2114

Alfa AF: 0.0684 Hom.: 46

Bravo AF: 0.0723

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.76
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7216369; hg19: chr17-12860315; COSMIC: COSV52400601;