Variant X-7843210-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001393662.1(VCX):c.7C>T(p.Pro3Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0025 ( 0 hom., 0 hem., cov: 19)

Exomes 𝑓: 0.0043 ( 0 hom. 48 hem. )

Failed GnomAD Quality Control

Consequence

VCX
NM_001393662.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0900

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 Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008450568).

BP6

Variant X-7843210-C-T is Benign according to our data. Variant chrX-7843210-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3025302.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
VCX	NM_001393662.1 linkuse as main transcript	c.7C>T	p.Pro3Ser	missense_variant	1/2	ENST00000688183.1	NP_001380591.1
VCX	NM_013452.3 linkuse as main transcript	c.7C>T	p.Pro3Ser	missense_variant	2/3		NP_038480.2
VCX	XM_011545490.4 linkuse as main transcript	c.7C>T	p.Pro3Ser	missense_variant	1/3		XP_011543792.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VCX	ENST00000688183.1 linkuse as main transcript	c.7C>T	p.Pro3Ser	missense_variant	1/2		NM_001393662.1	ENSP00000509688	P1

Frequencies

GnomAD3 genomes

AF:

0.00255

AC:

251

AN:

98506

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

24116

show subpopulations

Gnomad AFR

AF:

0.000433

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00574

Gnomad ASJ

AF:

0.00129

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000651

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00374

Gnomad OTH

AF:

0.00157

GnomAD3 exomes

AF:

0.000833

AC:

126

AN:

151242

Hom.:

AF XY:

0.000105

AC XY:

AN XY:

47396

show subpopulations

Gnomad AFR exome

AF:

0.000280

Gnomad AMR exome

AF:

0.000607

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000268

Gnomad FIN exome

AF:

0.000147

Gnomad NFE exome

AF:

0.00148

Gnomad OTH exome

AF:

0.00133

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00435

AC:

4659

AN:

1071488

Hom.:

Cov.:

AF XY:

0.000138

AC XY:

AN XY:

348952

show subpopulations

Gnomad4 AFR exome

AF:

0.000572

Gnomad4 AMR exome

AF:

0.00204

Gnomad4 ASJ exome

AF:

0.00132

Gnomad4 EAS exome

AF:

0.0000332

Gnomad4 SAS exome

AF:

0.000410

Gnomad4 FIN exome

AF:

0.00123

Gnomad4 NFE exome

AF:

0.00524

Gnomad4 OTH exome

AF:

0.00371

GnomAD4 genome

AF:

0.00255

AC:

251

AN:

98543

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

24157

show subpopulations

Gnomad4 AFR

AF:

0.000432

Gnomad4 AMR

AF:

0.00573

Gnomad4 ASJ

AF:

0.00129

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000651

Gnomad4 NFE

AF:

0.00374

Gnomad4 OTH

AF:

0.00155

Alfa

AF:

0.00254

Hom.:

ESP6500AA

AF:

0.000529

AC:

ESP6500EA

AF:

0.00608

AC:

ExAC

AF:

0.00383

AC:

423

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

Feb 01, 2024

VCX: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.014

T;.;.

FATHMM_MKL

Benign

0.40

LIST_S2

Benign

0.65

T;T;T

M_CAP

Benign

0.0018

MetaRNN

Benign

0.0085

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.3

M;.;.

MutationTaster

Benign

1.0

N;N

PrimateAI

Uncertain

0.49

PROVEAN

Benign

-0.55

N;.;N

REVEL

Benign

0.021

Sift

Pathogenic

0.0

D;.;D

Sift4G

Uncertain

0.014

D;D;T

Polyphen

0.99

D;.;.

Vest4

0.11

MVP

0.043

MPC

0.36

ClinPred

0.020

GERP RS

0.17

Varity_R

0.14

gMVP

0.0079

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