X-8170151-G-A

Variant names:

• chrX-8170151-G-A
• rs139945143
• NM_016378.3:c.301C>T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_016378.3(VCX2):​c.301C>T​(p.His101Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000009 in 1,111,369 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H101N) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000053 (0 hom., 0 hem., cov: 8)
  • Exomes 𝑓: 0.0000066 (0 hom. 2 hem.)
• Consequence: VCX2 NM_016378.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905
• 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: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.06910527).
• BS2: High Hemizygotes in GnomAdExome4 at 2 gene

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.301C>T	p.His101Tyr	missense	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.301C>T	p.His101Tyr	missense	Exon 3 of 3	ENSP00000321309.4	Q9H322
	ENSG00000285679	ENST00000649338.1		n.263-58184G>A		intron	N/A
	ENSG00000285679	ENST00000659022.1		n.972-58184G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000534 AC: 3 AN: 56170 Hom.: 0 Cov.: 8

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000963

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000110 AC: 1 AN: 90793 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000716

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000663 AC: 7 AN: 1055207 Hom.: 0 Cov.: 30 AF XY: 0.00000593 AC XY: 2 AN XY: 337137

African (AFR) AF: 0.00 AC: 0 AN: 25380

American (AMR) AF: 0.0000306 AC: 1 AN: 32641

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18719

East Asian (EAS) AF: 0.00 AC: 0 AN: 29390

South Asian (SAS) AF: 0.0000195 AC: 1 AN: 51259

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37114

Middle Eastern (MID) AF: 0.000354 AC: 1 AN: 2828

European-Non Finnish (NFE) AF: 0.00000492 AC: 4 AN: 813527

Other (OTH) AF: 0.00 AC: 0 AN: 44349

GnomAD4 genome AF: 0.0000534 AC: 3 AN: 56162 Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0 AN XY: 6526

African (AFR) AF: 0.00 AC: 0 AN: 13418

American (AMR) AF: 0.00 AC: 0 AN: 4127

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1694

East Asian (EAS) AF: 0.00 AC: 0 AN: 1361

South Asian (SAS) AF: 0.00 AC: 0 AN: 843

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2509

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 81

European-Non Finnish (NFE) AF: 0.0000963 AC: 3 AN: 31137

Other (OTH) AF: 0.00 AC: 0 AN: 621

Alfa AF: 0.00 Hom.: 0

ExAC AF: 0.0000498 AC: 5

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.41	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	2.7
DANN	Benign	0.78
DEOGEN2	Benign	0.0075	T
FATHMM_MKL	Benign	0.0029	N
LIST_S2	Benign	0.51	T
M_CAP	Benign	0.0011	T
MetaRNN	Benign	0.069	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.8	L
PhyloP100		0.91
PrimateAI	Uncertain	0.53	T
PROVEAN	Uncertain	-2.8	D
REVEL	Benign	0.094
Sift	Benign	0.042	D
Sift4G	Uncertain	0.042	D
Polyphen		0.39	B
Vest4		0.29
MutPred		0.13		Gain of phosphorylation at H101 (P = 0.0041)
MVP		0.040
MPC		0.0090
ClinPred		0.21	T
GERP RS		0.046
Varity_R		0.22
gMVP		0.0014
Mutation Taster		=100/0	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: rs139945143; hg19: chrX-8138192;