rs17215817

Positions:

• chr8-130407414-G-A

Variant summary

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

The NM_018482.4(ASAP1):​c.-27-5444C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,088 control chromosomes in the GnomAD database, including 12,344 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 (12344 hom., cov: 32)
• Consequence: ASAP1 NM_018482.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASAP1	NM_018482.4	c.-27-5444C>T		intron_variant		ENST00000518721.6	NP_060952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASAP1	ENST00000518721.6	c.-27-5444C>T		intron_variant		5	NM_018482.4	ENSP00000429900.1
ASAP1	ENST00000357668.2	c.-150-5444C>T		intron_variant		5		ENSP00000350297.2
ASAP1	ENST00000520927.5	n.-27-5444C>T		intron_variant		5		ENSP00000428629.1
ASAP1	ENST00000524299.1	n.-27-5444C>T		intron_variant		4		ENSP00000429614.1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57232 AN: 151970 Hom.: 12319 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.377 AC: 57319 AN: 152088 Hom.: 12344 Cov.: 32 AF XY: 0.367 AC XY: 27266 AN XY: 74358

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0731

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.346

Alfa AF: 0.363 Hom.: 1342

Bravo AF: 0.386

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.99
DANN	Benign	0.44

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: rs17215817; hg19: chr8-131419660;