Variant chr2-235709225-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001037131.3(AGAP1):c.210G>A(p.Pro70=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0134 in 1,613,930 control chromosomes in the GnomAD database, including 2,442 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.070 ( 1275 hom., cov: 32)

Exomes 𝑓: 0.0075 ( 1167 hom. )

Consequence

AGAP1
NM_001037131.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.65

Variant links:

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]

AGAP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 2-235709225-G-A is Benign according to our data. Variant chr2-235709225-G-A is described in ClinVar as [Benign]. Clinvar id is 2003469.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.65 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
AGAP1	NM_001037131.3 linkuse as main transcript	c.210G>A	p.Pro70=	synonymous_variant	2/18	ENST00000304032.13
AGAP1	NM_014914.5 linkuse as main transcript	c.210G>A	p.Pro70=	synonymous_variant	2/17
AGAP1	NM_001244888.2 linkuse as main transcript	c.210G>A	p.Pro70=	synonymous_variant	2/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGAP1	ENST00000304032.13 linkuse as main transcript	c.210G>A	p.Pro70=	synonymous_variant	2/18	5	NM_001037131.3		Q9UPQ3-1

Frequencies

GnomAD3 genomes

AF:

0.0703

AC:

10678

AN:

151986

Hom.:

1275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0272

Gnomad ASJ

AF:

0.00635

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000831

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00106

Gnomad OTH

AF:

0.0551

GnomAD3 exomes

AF:

0.0186

AC:

4676

AN:

251444

Hom.:

523

AF XY:

0.0135

AC XY:

1836

AN XY:

135900

show subpopulations

Gnomad AFR exome

AF:

0.246

Gnomad AMR exome

AF:

0.0126

Gnomad ASJ exome

AF:

0.00506

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000653

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.000870

Gnomad OTH exome

AF:

0.0108

GnomAD4 exome

AF:

0.00754

AC:

11017

AN:

1461826

Hom.:

1167

Cov.:

AF XY:

0.00649

AC XY:

4723

AN XY:

727222

show subpopulations

Gnomad4 AFR exome

AF:

0.250

Gnomad4 AMR exome

AF:

0.0145

Gnomad4 ASJ exome

AF:

0.00582

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000568

Gnomad4 FIN exome

AF:

0.0000749

Gnomad4 NFE exome

AF:

0.000645

Gnomad4 OTH exome

AF:

0.0168

GnomAD4 genome

AF:

0.0703

AC:

10688

AN:

152104

Hom.:

1275

Cov.:

AF XY:

0.0677

AC XY:

5031

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.243

Gnomad4 AMR

AF:

0.0272

Gnomad4 ASJ

AF:

0.00635

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000832

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00106

Gnomad4 OTH

AF:

0.0546

Alfa

AF:

0.0320

Hom.:

267

Bravo

AF:

0.0801

Asia WGS

AF:

0.0110

AC:

AN:

3478

EpiCase

AF:

0.00120

EpiControl

AF:

0.000889

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

5.2

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over