2-235620294-A-T

Variant names:

• chr2-235620294-A-T
• rs10199178
• NM_001037131.3:c.164-88885A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001037131.3(AGAP1):​c.164-88885A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151,526 control chromosomes in the GnomAD database, including 6,475 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 0.27 (6475 hom., cov: 32)
• Consequence: AGAP1 NM_001037131.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001037131.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGAP1	NM_001037131.3	MANE Select	c.164-88885A>T		intron	N/A	NP_001032208.1
	AGAP1	NM_014914.5		c.164-88885A>T		intron	N/A	NP_055729.2
	AGAP1	NM_001244888.2		c.164-88885A>T		intron	N/A	NP_001231817.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGAP1	ENST00000304032.13	TSL:5 MANE Select	c.164-88885A>T		intron	N/A	ENSP00000307634.7
	AGAP1	ENST00000336665.9	TSL:1	c.164-88885A>T		intron	N/A	ENSP00000338378.5
	AGAP1	ENST00000409457.5	TSL:1	c.164-88885A>T		intron	N/A	ENSP00000387174.1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41382 AN: 151406 Hom.: 6473 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.00352

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.273 AC: 41423 AN: 151526 Hom.: 6475 Cov.: 32 AF XY: 0.268 AC XY: 19819 AN XY: 74004

African (AFR) AF: 0.413 AC: 17089 AN: 41348

American (AMR) AF: 0.195 AC: 2974 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 934 AN: 3464

East Asian (EAS) AF: 0.00353 AC: 18 AN: 5106

South Asian (SAS) AF: 0.146 AC: 696 AN: 4780

European-Finnish (FIN) AF: 0.216 AC: 2265 AN: 10510

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16544 AN: 67774

Other (OTH) AF: 0.281 AC: 589 AN: 2098

Alfa AF: 0.249 Hom.: 615

Bravo AF: 0.279

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.48
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

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: rs10199178; hg19: chr2-236528938;