Variant 9-125312528-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001282680.3(GAPVD1):c.1518T>C(p.Ile506Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.955 in 1,610,904 control chromosomes in the GnomAD database, including 734,227 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.97 ( 71306 hom., cov: 31)

Exomes 𝑓: 0.95 ( 662921 hom. )

Consequence

GAPVD1
NM_001282680.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.0390

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 9-125312528-T-C is Benign according to our data. Variant chr9-125312528-T-C is described in ClinVar as [Benign]. Clinvar id is 3060575.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.039 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 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.1518T>C	p.Ile506Ile	synonymous_variant	9/28	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.1518T>C	p.Ile506Ile	synonymous_variant	9/28	1	NM_001282680.3	ENSP00000297933.6		Q14C86-2

Frequencies

GnomAD3 genomes

AF:

0.967

AC:

147182

AN:

152158

Hom.:

71244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.991

Gnomad AMI

AF:

0.961

Gnomad AMR

AF:

0.962

Gnomad ASJ

AF:

0.976

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.992

Gnomad FIN

AF:

0.978

Gnomad MID

AF:

0.978

Gnomad NFE

AF:

0.948

Gnomad OTH

AF:

0.969

GnomAD3 exomes

AF:

0.967

AC:

240664

AN:

248854

Hom.:

116418

AF XY:

0.967

AC XY:

130199

AN XY:

134578

show subpopulations

Gnomad AFR exome

AF:

0.991

Gnomad AMR exome

AF:

0.979

Gnomad ASJ exome

AF:

0.977

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.993

Gnomad FIN exome

AF:

0.975

Gnomad NFE exome

AF:

0.946

Gnomad OTH exome

AF:

0.964

GnomAD4 exome

AF:

0.953

AC:

1390432

AN:

1458628

Hom.:

662921

Cov.:

AF XY:

0.955

AC XY:

692736

AN XY:

725652

show subpopulations

Gnomad4 AFR exome

AF:

0.993

Gnomad4 AMR exome

AF:

0.978

Gnomad4 ASJ exome

AF:

0.977

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.992

Gnomad4 FIN exome

AF:

0.971

Gnomad4 NFE exome

AF:

0.944

Gnomad4 OTH exome

AF:

0.963

GnomAD4 genome

AF:

0.967

AC:

147303

AN:

152276

Hom.:

71306

Cov.:

AF XY:

0.969

AC XY:

72160

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.991

Gnomad4 AMR

AF:

0.962

Gnomad4 ASJ

AF:

0.976

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.992

Gnomad4 FIN

AF:

0.978

Gnomad4 NFE

AF:

0.948

Gnomad4 OTH

AF:

0.970

Alfa

AF:

0.954

Hom.:

111859

Bravo

AF:

0.967

Asia WGS

AF:

0.997

AC:

3466

AN:

3478

EpiCase

AF:

0.953

EpiControl

AF:

0.953

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

FAM157B-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 18, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

9.3

DANN

Benign

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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