rs2620636

chr8-144552744-C-T

Variant summary

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

The NM_025251.3(ARHGAP39):c.596+2816G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,114 control chromosomes in the GnomAD database, including 1,402 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 0.10 (1402 hom., cov: 33)
• Consequence: ARHGAP39 NM_025251.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

ARHGAP39 (HGNC:29351): (Rho GTPase activating protein 39) Predicted to enable GTPase activator activity. Involved in postsynapse organization. Is active in glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP39	NM_025251.3	c.596+2816G>A		intron_variant		ENST00000377307.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP39	ENST00000377307.7	c.596+2816G>A		intron_variant		5	NM_025251.3
ARHGAP39	ENST00000276826.5	c.596+2816G>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15400 AN: 151996 Hom.: 1392 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0930

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0904

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

GnomAD4 genome AF: 0.102 AC: 15455 AN: 152114 Hom.: 1402 Cov.: 33 AF XY: 0.0998 AC XY: 7422 AN XY: 74386

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0930

Gnomad4 EAS AF: 0.00675

Gnomad4 SAS AF: 0.0887

Gnomad4 FIN AF: 0.0136

Gnomad4 NFE AF: 0.0426

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.0619 Hom.: 241

Bravo AF: 0.115

Asia WGS AF: 0.0560 AC: 195 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	0.17
Dann	Benign	0.19

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: rs2620636; hg19: chr8-145778128;