Variant X-7843611-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001393662.1(VCX):c.216G>A(p.Ala72=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000063 ( 0 hom., 0 hem., cov: 10)

Exomes 𝑓: 0.00045 ( 11 hom. 49 hem. )

Failed GnomAD Quality Control

Consequence

VCX
NM_001393662.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.162

Variant links:

Genes affected

VCX (HGNC:12667): (variable charge X-linked) This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes, and all are expressed exclusively in male germ cells. The X-linked members are clustered on chromosome Xp22 and Y-linked members are two identical copies of the gene within a palindromic region on Yq11. The family members share a high degree of sequence identity, with the exception that a 30-bp unit is tandemly repeated in X-linked members but occurs only once in Y-linked members. The VCX gene cluster is polymorphic in terms of copy number; different individuals may have a different number of VCX genes. VCX/Y genes encode small and highly charged proteins of unknown function. The presence of a putative bipartite nuclear localization signal suggests that VCX/Y members are nuclear proteins. This gene contains 10 repeats of the 30-bp unit. [provided by RefSeq, Jul 2008]

VCX links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant X-7843611-G-A is Benign according to our data. Variant chrX-7843611-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2659918.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.162 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
VCX	NM_001393662.1 linkuse as main transcript	c.216G>A	p.Ala72=	synonymous_variant	2/2	ENST00000688183.1	NP_001380591.1
VCX	NM_013452.3 linkuse as main transcript	c.216G>A	p.Ala72=	synonymous_variant	3/3		NP_038480.2
VCX	XM_011545490.4 linkuse as main transcript	c.216G>A	p.Ala72=	synonymous_variant	2/3		XP_011543792.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VCX	ENST00000688183.1 linkuse as main transcript	c.216G>A	p.Ala72=	synonymous_variant	2/2		NM_001393662.1	ENSP00000509688	P1

Frequencies

GnomAD3 genomes

AF:

0.0000625

AC:

AN:

63981

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

12043

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000194

Gnomad ASJ

AF:

0.000684

Gnomad EAS

AF:

0.000442

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000324

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000423

AC:

AN:

146476

Hom.:

AF XY:

0.000150

AC XY:

AN XY:

46566

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000326

Gnomad ASJ exome

AF:

0.00193

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000615

Gnomad FIN exome

AF:

0.0000771

Gnomad NFE exome

AF:

0.000605

Gnomad OTH exome

AF:

0.000806

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000448

AC:

467

AN:

1042752

Hom.:

Cov.:

AF XY:

0.000152

AC XY:

AN XY:

322074

show subpopulations

Gnomad4 AFR exome

AF:

0.0000774

Gnomad4 AMR exome

AF:

0.000331

Gnomad4 ASJ exome

AF:

0.00118

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000386

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000506

Gnomad4 OTH exome

AF:

0.000547

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000625

AC:

AN:

63987

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

12065

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000195

Gnomad4 ASJ

AF:

0.000684

Gnomad4 EAS

AF:

0.000445

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000324

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000831

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

VCX: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.8

DANN

Benign

0.68

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