NM_018482.4:c.2401+1696A>G

Variant names:

• chr8-130110398-T-C
• rs3812476
• NM_018482.4:c.2401+1696A>G

Variant summary

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

The NM_018482.4(ASAP1):​c.2401+1696A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,170 control chromosomes in the GnomAD database, including 2,635 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 0.16 (2635 hom., cov: 31)
• Consequence: ASAP1 NM_018482.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.84
• Publications: 4 publications found

Genes affected

ASAP1 (HGNC:2720): (ArfGAP with SH3 domain, ankyrin repeat and PH domain 1) This gene encodes an ADP-ribosylation factor (ARF) GTPase-activating protein. The GTPase-activating activity is stimulated by phosphatidylinositol 4,5-biphosphate (PIP2), and is greater towards ARF1 and ARF5, and lesser for ARF6. This gene maybe involved in regulation of membrane trafficking and cytoskeleton remodeling. Alternatively spliced 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASAP1	NM_018482.4	c.2401+1696A>G		intron_variant	Intron 24 of 29	ENST00000518721.6	NP_060952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASAP1	ENST00000518721.6	c.2401+1696A>G		intron_variant	Intron 24 of 29	5	NM_018482.4	ENSP00000429900.1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24753 AN: 152056 Hom.: 2637 Cov.: 31

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.163 AC: 24752 AN: 152170 Hom.: 2635 Cov.: 31 AF XY: 0.166 AC XY: 12326 AN XY: 74378

African (AFR) AF: 0.0542 AC: 2253 AN: 41554

American (AMR) AF: 0.252 AC: 3851 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1091 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2274 AN: 5158

South Asian (SAS) AF: 0.234 AC: 1125 AN: 4816

European-Finnish (FIN) AF: 0.0994 AC: 1053 AN: 10596

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12469 AN: 67990

Other (OTH) AF: 0.198 AC: 418 AN: 2114

Alfa AF: 0.169 Hom.: 443

Bravo AF: 0.172

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.027
DANN	Benign	0.61
PhyloP100		-3.8
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: rs3812476; hg19: chr8-131122644;