rs1881187

Variant names:

• chr2-235659086-G-A
• rs1881187
• NM_001037131.3:c.164-50093G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-235659086-G-A
• chr2-235659086-G-C
• chr2-235659086-G-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.164-50093G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,010 control chromosomes in the GnomAD database, including 42,962 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 0.74 (42962 hom., cov: 32)
• Consequence: AGAP1 NM_001037131.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGAP1	NM_001037131.3	c.164-50093G>A		intron_variant	Intron 1 of 17	ENST00000304032.13	NP_001032208.1
AGAP1	NM_014914.5	c.164-50093G>A		intron_variant	Intron 1 of 16		NP_055729.2
AGAP1	NM_001244888.2	c.164-50093G>A		intron_variant	Intron 1 of 9		NP_001231817.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGAP1	ENST00000304032.13	c.164-50093G>A		intron_variant	Intron 1 of 17	5	NM_001037131.3	ENSP00000307634.7

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112685 AN: 151892 Hom.: 42901 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.742 AC: 112799 AN: 152010 Hom.: 42962 Cov.: 32 AF XY: 0.739 AC XY: 54912 AN XY: 74298

African (AFR) AF: 0.918 AC: 38080 AN: 41504

American (AMR) AF: 0.778 AC: 11893 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2563 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4161 AN: 5126

South Asian (SAS) AF: 0.641 AC: 3075 AN: 4800

European-Finnish (FIN) AF: 0.568 AC: 5992 AN: 10544

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44684 AN: 67962

Other (OTH) AF: 0.745 AC: 1574 AN: 2112

Alfa AF: 0.719 Hom.: 6762

Bravo AF: 0.767

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.49
PhyloP100		-0.68
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: rs1881187; hg19: chr2-236567730;