Variant 9-125305140-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001282680.3(GAPVD1):c.1107G>A(p.Lys369Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 1,605,182 control chromosomes in the GnomAD database, including 963 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.047 ( 499 hom., cov: 33)

Exomes 𝑓: 0.0083 ( 464 hom. )

Consequence

GAPVD1
NM_001282680.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.01

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 9-125305140-G-A is Benign according to our data. Variant chr9-125305140-G-A is described in ClinVar as [Benign]. Clinvar id is 1270828.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.01 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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.1107G>A	p.Lys369Lys	synonymous_variant	6/28	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.1107G>A	p.Lys369Lys	synonymous_variant	6/28	1	NM_001282680.3	ENSP00000297933.6		Q14C86-2

Frequencies

GnomAD3 genomes

AF:

0.0470

AC:

7148

AN:

152124

Hom.:

499

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0206

Gnomad ASJ

AF:

0.00980

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00539

Gnomad FIN

AF:

0.000847

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00442

Gnomad OTH

AF:

0.0425

GnomAD3 exomes

AF:

0.0151

AC:

3792

AN:

251204

Hom.:

203

AF XY:

0.0124

AC XY:

1680

AN XY:

135782

show subpopulations

Gnomad AFR exome

AF:

0.156

Gnomad AMR exome

AF:

0.0136

Gnomad ASJ exome

AF:

0.00944

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00438

Gnomad FIN exome

AF:

0.000554

Gnomad NFE exome

AF:

0.00400

Gnomad OTH exome

AF:

0.0150

GnomAD4 exome

AF:

0.00828

AC:

12026

AN:

1452940

Hom.:

464

Cov.:

AF XY:

0.00772

AC XY:

5585

AN XY:

723500

show subpopulations

Gnomad4 AFR exome

AF:

0.158

Gnomad4 AMR exome

AF:

0.0147

Gnomad4 ASJ exome

AF:

0.00948

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00455

Gnomad4 FIN exome

AF:

0.000693

Gnomad4 NFE exome

AF:

0.00380

Gnomad4 OTH exome

AF:

0.0164

GnomAD4 genome

AF:

0.0470

AC:

7162

AN:

152242

Hom.:

499

Cov.:

AF XY:

0.0455

AC XY:

3386

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.154

Gnomad4 AMR

AF:

0.0206

Gnomad4 ASJ

AF:

0.00980

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00498

Gnomad4 FIN

AF:

0.000847

Gnomad4 NFE

AF:

0.00441

Gnomad4 OTH

AF:

0.0421

Alfa

AF:

0.0230

Hom.:

116

Bravo

AF:

0.0541

Asia WGS

AF:

0.0160

AC:

AN:

3478

EpiCase

AF:

0.00578

EpiControl

AF:

0.00599

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 04, 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

-0.41

CADD

Benign

7.0

DANN

Benign

0.80

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.9

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