rs10956514

Positions:

• chr8-130240512-A-G

Variant summary

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

The NM_018482.4(ASAP1):​c.187-3518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,940 control chromosomes in the GnomAD database, including 11,361 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 0.38 (11361 hom., cov: 32)
• Consequence: ASAP1 NM_018482.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASAP1	NM_018482.4	c.187-3518T>C		intron_variant		ENST00000518721.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASAP1	ENST00000518721.6	c.187-3518T>C		intron_variant		5	NM_018482.4	P2

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57441 AN: 151822 Hom.: 11356 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.378 AC: 57465 AN: 151940 Hom.: 11361 Cov.: 32 AF XY: 0.383 AC XY: 28470 AN XY: 74258

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.427

Alfa AF: 0.411 Hom.: 12100

Bravo AF: 0.378

Asia WGS AF: 0.497 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.84

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: rs10956514; hg19: chr8-131252758; COSMIC: COSV63050129; COSMIC: COSV63050129;