X-6533828-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000381089.7(VCX3A):c.478G>A(p.Val160Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.16 ( 1 hom., 1 hem., cov: 10)
Exomes 𝑓: 0.0047 ( 2 hom. 71 hem. )
Failed GnomAD Quality Control
Consequence
VCX3A
ENST00000381089.7 missense
ENST00000381089.7 missense
Scores
16
Clinical Significance
Conservation
PhyloP100: -0.446
Genes affected
VCX3A (HGNC:18159): (variable charge X-linked 3A) 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 8 repeats of the 30-bp unit. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0018401444).
BP6
Variant X-6533828-C-T is Benign according to our data. Variant chrX-6533828-C-T is described in ClinVar as [Benign]. Clinvar id is 252705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-6533828-C-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCX3A | NM_016379.4 | c.478G>A | p.Val160Met | missense_variant | 3/3 | ENST00000381089.7 | NP_057463.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VCX3A | ENST00000381089.7 | c.478G>A | p.Val160Met | missense_variant | 3/3 | 1 | NM_016379.4 | ENSP00000370479.3 | ||
VCX3A | ENST00000398729.1 | c.418G>A | p.Val140Met | missense_variant | 4/4 | 5 | ENSP00000381713.1 |
Frequencies
GnomAD3 genomes AF: 0.164 AC: 7418AN: 45196Hom.: 1 Cov.: 10 AF XY: 0.000119 AC XY: 1AN XY: 8392
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GnomAD3 exomes AF: 0.0225 AC: 2046AN: 91027Hom.: 10 AF XY: 0.000968 AC XY: 31AN XY: 32033
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00467 AC: 3611AN: 772846Hom.: 2 Cov.: 49 AF XY: 0.000290 AC XY: 71AN XY: 245250
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.164 AC: 7410AN: 45177Hom.: 1 Cov.: 10 AF XY: 0.000119 AC XY: 1AN XY: 8395
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Nov 19, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
P;.
Vest4
MPC
ClinPred
T
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at