chr8-130317591-C-T

Variant names:

• chr8-130317591-C-T
• rs3057
• NM_018482.4:c.186+40426G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.87).
• 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 rank	MANE	Protein	UniProt
ASAP1	NM_018482.4	c.186+40426G>A		intron_variant	Intron 3 of 29	ENST00000518721.6	NP_060952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASAP1	ENST00000518721.6	c.186+40426G>A		intron_variant	Intron 3 of 29	5	NM_018482.4	ENSP00000429900.1

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

African (AFR) AF: 0.625 AC: 25923 AN: 41504

American (AMR) AF: 0.612 AC: 9359 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2077 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3508 AN: 5172

South Asian (SAS) AF: 0.701 AC: 3388 AN: 4830

European-Finnish (FIN) AF: 0.497 AC: 5257 AN: 10572

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.551 AC: 37427 AN: 67952

Other (OTH) AF: 0.624 AC: 1316 AN: 2110

Alfa AF: 0.567 Hom.: 12680

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
PhyloP100		-1.5
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: rs3057; hg19: chr8-131329837;