NM_001037131.3:c.1051-13010G>A

Variant names:

• chr2-235870335-G-A
• rs6759206
• NM_001037131.3:c.1051-13010G>A

Variant summary

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

The NM_001037131.3(AGAP1):​c.1051-13010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 152,058 control chromosomes in the GnomAD database, including 18,313 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 0.49 (18313 hom., cov: 33)
• Consequence: AGAP1 NM_001037131.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 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.1051-13010G>A		intron	N/A	NP_001032208.1
	AGAP1	NM_001436125.1		c.1846-13010G>A		intron	N/A	NP_001423054.1
	AGAP1	NM_001436126.1		c.1846-13010G>A		intron	N/A	NP_001423055.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGAP1	ENST00000304032.13	TSL:5 MANE Select	c.1051-13010G>A		intron	N/A	ENSP00000307634.7
	AGAP1	ENST00000336665.9	TSL:1	c.1051-13010G>A		intron	N/A	ENSP00000338378.5
	AGAP1	ENST00000409538.5	TSL:5	c.1846-13010G>A		intron	N/A	ENSP00000386897.1

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73803 AN: 151938 Hom.: 18280 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.486 AC: 73893 AN: 152058 Hom.: 18313 Cov.: 33 AF XY: 0.482 AC XY: 35839 AN XY: 74328

African (AFR) AF: 0.524 AC: 21715 AN: 41476

American (AMR) AF: 0.408 AC: 6231 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1884 AN: 3470

East Asian (EAS) AF: 0.554 AC: 2857 AN: 5160

South Asian (SAS) AF: 0.736 AC: 3543 AN: 4814

European-Finnish (FIN) AF: 0.386 AC: 4088 AN: 10582

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31944 AN: 67950

Other (OTH) AF: 0.485 AC: 1025 AN: 2114

Alfa AF: 0.486 Hom.: 13338

Bravo AF: 0.486

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.71
PhyloP100		-0.83
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: rs6759206; hg19: chr2-236778979;