NM_025251.3:c.596+2816G>T

Variant names:

• chr8-144552744-C-A
• rs2620636
• NM_025251.3:c.596+2816G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_025251.3(ARHGAP39):​c.596+2816G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ARHGAP39 NM_025251.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 0 publications found

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]

ARHGAP39 Gene-Disease associations (from GenCC):

• central nervous system malformation

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025251.3. 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
	ARHGAP39	NM_025251.3	MANE Select	c.596+2816G>T		intron	N/A	NP_079527.1
	ARHGAP39	NM_001308207.1		c.596+2816G>T		intron	N/A	NP_001295136.1
	ARHGAP39	NM_001308208.2		c.596+2816G>T		intron	N/A	NP_001295137.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP39	ENST00000377307.7	TSL:5 MANE Select	c.596+2816G>T		intron	N/A	ENSP00000366522.2
	ARHGAP39	ENST00000905351.1		c.596+2816G>T		intron	N/A	ENSP00000575410.1
	ARHGAP39	ENST00000905352.1		c.596+2816G>T		intron	N/A	ENSP00000575411.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.23
PhyloP100		-1.7

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: rs2620636; hg19: chr8-145778128;