chrX-52813173-C-T

Variant names:

• chrX-52813173-C-T
• NM_001386970.1:c.106C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001386970.1(XAGE5):​c.106C>T​(p.Pro36Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: XAGE5 NM_001386970.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.0980
• Publications: 0 publications found

Genes affected

XAGE5 (HGNC:30930): (X antigen family member 5) This gene is a member of the XAGE subfamily, which belongs to the GAGE family. The GAGE genes are expressed in a variety of tumors and in some fetal and reproductive tissues. The protein encoded by this gene shares a sequence similarity with other GAGE/PAGE proteins. Because of the expression pattern and the sequence similarity, this protein also belongs to a family of CT (cancer-testis) antigens. [provided by RefSeq, Jul 2008]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10323024).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001386970.1. 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
	XAGE5	NM_001386970.1	MANE Select	c.106C>T	p.Pro36Ser	missense	Exon 4 of 6	NP_001373899.1	Q8WWM1
	XAGE5	NM_130775.3		c.106C>T	p.Pro36Ser	missense	Exon 3 of 5	NP_570131.1	Q8WWM1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XAGE5	ENST00000375501.2	TSL:5 MANE Select	c.106C>T	p.Pro36Ser	missense	Exon 4 of 6	ENSP00000364651.1	Q8WWM1
	XAGE5	ENST00000375503.7	TSL:1	n.106C>T		non_coding_transcript_exon	Exon 2 of 5	ENSP00000364653.3	Q3SY49

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.095
BayesDel_addAF	Benign	-0.45	T
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.34
DEOGEN2	Benign	0.036	T
FATHMM_MKL	Benign	0.0018	N
LIST_S2	Benign	0.62	T
M_CAP	Benign	0.00044	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	2.0	M
PhyloP100		-0.098
PrimateAI	Benign	0.32	T
PROVEAN	Pathogenic	-5.8	D
REVEL	Benign	0.041
Sift	Benign	0.079	T
Sift4G	Uncertain	0.036	D
Polyphen		0.013	B
Vest4		0.21
MutPred		0.52		Loss of catalytic residue at P36 (P = 0.0019)
MVP		0.030
MPC		0.0028
ClinPred		0.080	T
GERP RS		-2.2
Varity_R		0.099
gMVP		0.025
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

hg19: chrX-52842197;