rs3812476

chr8-130110398-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ASAP1	NM_018482.4	c.2401+1696A>G		intron_variant		ENST00000518721.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASAP1	ENST00000518721.6	c.2401+1696A>G		intron_variant		5	NM_018482.4	P2

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

Gnomad4 AFR AF: 0.0542

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.0994

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.198

Alfa AF: 0.172 Hom.: 441

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

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: rs3812476; hg19: chr8-131122644;