chr1-23439740-C-T

Position:

• chr1-23439740-C-T

Variant summary

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

The NM_017707.4(ASAP3):​c.945-510G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,190 control chromosomes in the GnomAD database, including 44,518 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 0.75 (44518 hom., cov: 33)
• Consequence: ASAP3 NM_017707.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

Genes affected

ASAP3 (HGNC:14987): (ArfGAP with SH3 domain, ankyrin repeat and PH domain 3) This gene encodes a member of a subfamily of ADP-ribosylation factor(Arf) GTPase-activating proteins that contain additional ankyrin repeat and pleckstrin homology domains. The Arf GAP domain of this protein catalyzes the hydrolysis of GTP bound to Arf proteins. The encoded protein promotes cell differentiation and migration and has been implicated in cancer cell invasion. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASAP3	NM_017707.4	c.945-510G>A		intron_variant		ENST00000336689.8	NP_060177.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASAP3	ENST00000336689.8	c.945-510G>A		intron_variant		1	NM_017707.4	ENSP00000338769.3
ASAP3	ENST00000437606.6	c.918-510G>A		intron_variant		2		ENSP00000408826.2
ASAP3	ENST00000475814.5	n.360-906G>A		intron_variant		5		ENSP00000436439.1
ASAP3	ENST00000492982.6	n.*779-510G>A		intron_variant		2		ENSP00000435858.1

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113772 AN: 152072 Hom.: 44505 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.748 AC: 113824 AN: 152190 Hom.: 44518 Cov.: 33 AF XY: 0.748 AC XY: 55619 AN XY: 74406

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.801

Alfa AF: 0.842 Hom.: 81271

Bravo AF: 0.734

Asia WGS AF: 0.627 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	13
DANN	Benign	0.76

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: rs1077514; hg19: chr1-23766233;