rs13294021

chr9-125306109-G-Achr9-125306109-G-T

Variant summary

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

The NM_001282680.3(GAPVD1):c.1116+960G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,774 control chromosomes in the GnomAD database, including 16,089 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 0.45 (16089 hom., cov: 31)
• Consequence: GAPVD1 NM_001282680.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

GAPVD1 (HGNC:23375): (GTPase activating protein and VPS9 domains 1) Enables GTPase activating protein binding activity and guanyl-nucleotide exchange factor activity. Involved in regulation of protein transport. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAPVD1	NM_001282680.3	c.1116+960G>A		intron_variant		ENST00000297933.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAPVD1	ENST00000297933.11	c.1116+960G>A		intron_variant		1	NM_001282680.3	P3

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68839 AN: 151668 Hom.: 16082 Cov.: 31

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.454 AC: 68863 AN: 151774 Hom.: 16089 Cov.: 31 AF XY: 0.450 AC XY: 33389 AN XY: 74164

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.452

Alfa AF: 0.451 Hom.: 26059

Bravo AF: 0.443

Asia WGS AF: 0.301 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.15
Dann	Benign	0.50

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: rs13294021; hg19: chr9-128068388;