8-130317591-C-T

Position:

• chr8-130317591-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018482.4(ASAP1):​c.186+40426G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,092 control chromosomes in the GnomAD database, including 26,141 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 0.58 (26141 hom., cov: 32)
• Consequence: ASAP1 NM_018482.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASAP1	NM_018482.4	c.186+40426G>A		intron_variant		ENST00000518721.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASAP1	ENST00000518721.6	c.186+40426G>A		intron_variant		5	NM_018482.4	P2

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88847 AN: 151974 Hom.: 26099 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.585 AC: 88938 AN: 152092 Hom.: 26141 Cov.: 32 AF XY: 0.586 AC XY: 43551 AN XY: 74350

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.624

Alfa AF: 0.567 Hom.: 11317

Bravo AF: 0.594

Asia WGS AF: 0.658 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.050
DANN	Benign	0.69

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: rs3057; hg19: chr8-131329837;