NM_018482.4:c.-27-5444C>T

Variant names:

• chr8-130407414-G-A
• rs17215817
• NM_018482.4:c.-27-5444C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.89).
• 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 rank	MANE	Protein	UniProt
ASAP1	NM_018482.4	c.-27-5444C>T		intron_variant	Intron 1 of 29	ENST00000518721.6	NP_060952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASAP1	ENST00000518721.6	c.-27-5444C>T		intron_variant	Intron 1 of 29	5	NM_018482.4	ENSP00000429900.1
ASAP1	ENST00000357668.2	c.-150-5444C>T		intron_variant	Intron 1 of 30	5		ENSP00000350297.2
ASAP1	ENST00000520927.5	n.-27-5444C>T		intron_variant	Intron 1 of 8	5		ENSP00000428629.1
ASAP1	ENST00000524299.1	n.-27-5444C>T		intron_variant	Intron 1 of 5	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

African (AFR) AF: 0.588 AC: 24403 AN: 41478

American (AMR) AF: 0.318 AC: 4861 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3468

East Asian (EAS) AF: 0.0731 AC: 379 AN: 5184

South Asian (SAS) AF: 0.191 AC: 922 AN: 4818

European-Finnish (FIN) AF: 0.290 AC: 3068 AN: 10566

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21725 AN: 67982

Other (OTH) AF: 0.346 AC: 730 AN: 2108

Alfa AF: 0.372 Hom.: 1480

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
PhyloP100		-0.49
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: rs17215817; hg19: chr8-131419660;