Variant 9-125307598-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001282680.3(GAPVD1):c.1251+51G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0099 in 1,582,236 control chromosomes in the GnomAD database, including 704 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.020 ( 114 hom., cov: 32)

Exomes 𝑓: 0.0088 ( 590 hom. )

Consequence

GAPVD1
NM_001282680.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.42

Variant links:

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]

GAPVD1 links:

GAPVD1 (HGNC:):

GAPVD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 9-125307598-G-A is Benign according to our data. Variant chr9-125307598-G-A is described in ClinVar as [Benign]. Clinvar id is 1290078.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.081 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAPVD1	NM_001282680.3 linkuse as main transcript	c.1251+51G>A		intron_variant		ENST00000297933.11	NP_001269609.1	Q14C86-2A0A024R862

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAPVD1	ENST00000297933.11 linkuse as main transcript	c.1251+51G>A		intron_variant		1	NM_001282680.3	ENSP00000297933.6		Q14C86-2

Frequencies

GnomAD3 genomes

AF:

0.0197

AC:

3004

AN:

152142

Hom.:

110

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0262

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0839

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.0876

Gnomad SAS

AF:

0.0228

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000470

Gnomad OTH

AF:

0.0162

GnomAD3 exomes

AF:

0.0281

AC:

6884

AN:

244904

Hom.:

351

AF XY:

0.0242

AC XY:

3213

AN XY:

132550

show subpopulations

Gnomad AFR exome

AF:

0.0276

Gnomad AMR exome

AF:

0.121

Gnomad ASJ exome

AF:

0.00105

Gnomad EAS exome

AF:

0.0842

Gnomad SAS exome

AF:

0.0253

Gnomad FIN exome

AF:

0.0000470

Gnomad NFE exome

AF:

0.000359

Gnomad OTH exome

AF:

0.0198

GnomAD4 exome

AF:

0.00884

AC:

12643

AN:

1429976

Hom.:

590

Cov.:

AF XY:

0.00886

AC XY:

6304

AN XY:

711538

show subpopulations

Gnomad4 AFR exome

AF:

0.0270

Gnomad4 AMR exome

AF:

0.118

Gnomad4 ASJ exome

AF:

0.000547

Gnomad4 EAS exome

AF:

0.0955

Gnomad4 SAS exome

AF:

0.0244

Gnomad4 FIN exome

AF:

0.0000565

Gnomad4 NFE exome

AF:

0.000195

Gnomad4 OTH exome

AF:

0.00998

GnomAD4 genome

AF:

0.0199

AC:

3024

AN:

152260

Hom.:

114

Cov.:

AF XY:

0.0215

AC XY:

1604

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0267

Gnomad4 AMR

AF:

0.0841

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.0876

Gnomad4 SAS

AF:

0.0222

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.000485

Gnomad4 OTH

AF:

0.0156

Alfa

AF:

0.00388

Hom.:

Bravo

AF:

0.0264

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 17, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.010

DANN

Benign

0.58

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over