rs13025591

Positions:

• chr2-235886699-A-C
• chr2-235886699-A-G

Variant summary

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

The NM_001037131.3(AGAP1):​c.1155+3250A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,060 control chromosomes in the GnomAD database, including 10,909 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 0.37 (10909 hom., cov: 33)
• Consequence: AGAP1 NM_001037131.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

Genes affected

AGAP1 (HGNC:16922): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 1) This gene encodes a member of an ADP-ribosylation factor GTPase-activating protein family involved in membrane trafficking and cytoskeleton dynamics. This gene functions as a direct regulator of the adaptor-related protein complex 3 on endosomes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGAP1	NM_001037131.3	c.1155+3250A>C		intron_variant		ENST00000304032.13
AGAP1	NM_014914.5	c.1155+3250A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGAP1	ENST00000304032.13	c.1155+3250A>C		intron_variant		5	NM_001037131.3

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56412 AN: 151942 Hom.: 10903 Cov.: 33

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.371 AC: 56445 AN: 152060 Hom.: 10909 Cov.: 33 AF XY: 0.370 AC XY: 27506 AN XY: 74322

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.374

Alfa AF: 0.393 Hom.: 9043

Bravo AF: 0.365

Asia WGS AF: 0.547 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.80

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: rs13025591; hg19: chr2-236795343;