2-235952126-C-T

Position:

• chr2-235952126-C-T

Variant summary

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

The NM_001037131.3(AGAP1):​c.1484-16336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,992 control chromosomes in the GnomAD database, including 26,398 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 0.59 (26398 hom., cov: 32)
• Consequence: AGAP1 NM_001037131.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

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 = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGAP1	NM_001037131.3	c.1484-16336C>T		intron_variant		ENST00000304032.13
AGAP1	NM_014914.5	c.1325-16336C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGAP1	ENST00000304032.13	c.1484-16336C>T		intron_variant		5	NM_001037131.3

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88875 AN: 151874 Hom.: 26365 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.585 AC: 88958 AN: 151992 Hom.: 26398 Cov.: 32 AF XY: 0.588 AC XY: 43660 AN XY: 74274

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.586

Alfa AF: 0.566 Hom.: 4997

Bravo AF: 0.585

Asia WGS AF: 0.738 AC: 2564 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	0.044
DANN	Benign	0.26

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: rs2873333; hg19: chr2-236860770;