rs1569125

chr2-235647893-G-Achr2-235647893-G-C

Variant summary

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

The NM_001037131.3(AGAP1):c.164-61286G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 151,708 control chromosomes in the GnomAD database, including 36,744 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 0.70 (36744 hom., cov: 29)
• Consequence: AGAP1 NM_001037131.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGAP1	NM_001037131.3	c.164-61286G>A		intron_variant		ENST00000304032.13
AGAP1	NM_001244888.2	c.164-61286G>A		intron_variant
AGAP1	NM_014914.5	c.164-61286G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGAP1	ENST00000304032.13	c.164-61286G>A		intron_variant		5	NM_001037131.3

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105407 AN: 151590 Hom.: 36720 Cov.: 29

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.695 AC: 105475 AN: 151708 Hom.: 36744 Cov.: 29 AF XY: 0.692 AC XY: 51305 AN XY: 74110

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.729

Alfa AF: 0.700 Hom.: 5234

Bravo AF: 0.702

Asia WGS AF: 0.750 AC: 2610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.3
Dann	Benign	0.79

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: rs1569125; hg19: chr2-236556537;