chrX-8170178-C-A

Variant names:

• chrX-8170178-C-A
• rs759918077
• NM_016378.3:c.274G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_016378.3(VCX2):​c.274G>T​(p.Glu92*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 7)
  • Exomes 𝑓: 0.0000028 (0 hom. 3 hem.)
  • Failed GnomAD Quality Control
• Consequence: VCX2 NM_016378.3 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 0 publications found

Genes affected

VCX2 (HGNC:18158): (variable charge X-linked 2) This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes that are expressed exclusively in male germ cells. The VCX gene cluster is polymorphic in terms of copy number; different individuals may have a different number of VCX genes. This gene contains two copies of a 30 nt tandem repeat. Deletion of a nearby member of this family was implicated in cognitive disability. [provided by RefSeq, Feb 2015]

ENSG00000285679 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016378.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VCX2	NM_016378.3	MANE Select	c.274G>T	p.Glu92*	stop_gained	Exon 3 of 3	NP_057462.2	Q9H322

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VCX2	ENST00000317103.5	TSL:1 MANE Select	c.274G>T	p.Glu92*	stop_gained	Exon 3 of 3	ENSP00000321309.4	Q9H322
	ENSG00000285679	ENST00000649338.1		n.263-58157C>A		intron	N/A
	ENSG00000285679	ENST00000659022.1		n.972-58157C>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 7

GnomAD2 exomes AF: 0.0000126 AC: 2 AN: 158357 AF XY: 0.0000200

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000147

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000276 AC: 3 AN: 1087548 Hom.: 0 Cov.: 32 AF XY: 0.00000842 AC XY: 3 AN XY: 356088

African (AFR) AF: 0.00 AC: 0 AN: 26182

American (AMR) AF: 0.00 AC: 0 AN: 34649

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19221

East Asian (EAS) AF: 0.00 AC: 0 AN: 29960

South Asian (SAS) AF: 0.0000560 AC: 3 AN: 53603

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39163

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2874

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 836266

Other (OTH) AF: 0.00 AC: 0 AN: 45630

GnomAD4 genome Cov.: 7

ExAC AF: 0.0000168 AC: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.021	T
BayesDel_noAF	Uncertain	-0.030
CADD	Uncertain	24
DANN	Benign	0.97
FATHMM_MKL	Benign	0.0040	N
PhyloP100		-1.1
Vest4		0.058
GERP RS		0.046
Mutation Taster		=182/18	polymorphism

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

Other links and lift over

dbSNP: rs759918077; hg19: chrX-8138219;