rs10505547

Variant names:

• chr8-130116530-C-G
• rs10505547
• NM_018482.4:c.2064+148G>C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_018482.4(ASAP1):​c.2064+148G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00833 in 697,262 control chromosomes in the GnomAD database, including 35 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 0.0072 (8 hom., cov: 33)
  • Exomes 𝑓: 0.0087 (27 hom.)
• Consequence: ASAP1 NM_018482.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BS2: High AC in GnomAd4 at 1090 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASAP1	NM_018482.4	c.2064+148G>C		intron_variant	Intron 22 of 29	ENST00000518721.6	NP_060952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASAP1	ENST00000518721.6	c.2064+148G>C		intron_variant	Intron 22 of 29	5	NM_018482.4	ENSP00000429900.1

Frequencies

GnomAD3 genomes AF: 0.00717 AC: 1090 AN: 152128 Hom.: 8 Cov.: 33

Gnomad AFR AF: 0.00181

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00105

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.00143

GnomAD4 exome AF: 0.00866 AC: 4720 AN: 545016 Hom.: 27 AF XY: 0.00818 AC XY: 2346 AN XY: 286922

Gnomad4 AFR exome AF: 0.00114

Gnomad4 AMR exome AF: 0.000871

Gnomad4 ASJ exome AF: 0.00164

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000426

Gnomad4 FIN exome AF: 0.0211

Gnomad4 NFE exome AF: 0.0106

Gnomad4 OTH exome AF: 0.00623

GnomAD4 genome AF: 0.00716 AC: 1090 AN: 152246 Hom.: 8 Cov.: 33 AF XY: 0.00724 AC XY: 539 AN XY: 74438

Gnomad4 AFR AF: 0.00181

Gnomad4 AMR AF: 0.00105

Gnomad4 ASJ AF: 0.000864

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.0221

Gnomad4 NFE AF: 0.0111

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.0117 Hom.: 3

Bravo AF: 0.00508

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.7
DANN	Benign	0.85

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: rs10505547; hg19: chr8-131128776;