chrX-135778999-A-T

Position:

• chrX-135778999-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate

The NM_001007551.6(CT45A5):​c.431T>A​(p.Ile144Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: CT45A5 NM_001007551.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.83

Genes affected

CT45A5 (HGNC:33270): (cancer/testis antigen family 45 member A5) This gene represents one of a cluster of several similar genes located on the q arm of chromosome X. The genes in this cluster encode members of the cancer/testis (CT) family of antigens, and are distinct from other CT antigens. These antigens are thought to be novel therapeutic targets for human cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.895

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CT45A5	NM_001007551.6	c.431T>A	p.Ile144Asn	missense_variant	4/5	ENST00000698999.1	NP_001007552.2
CT45A5	NM_001172288.2	c.431T>A	p.Ile144Asn	missense_variant	4/5		NP_001165759.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CT45A5	ENST00000698999.1	c.431T>A	p.Ile144Asn	missense_variant	4/5		NM_001007551.6	ENSP00000514077.1
CT45A5	ENST00000617203.1	c.431T>A	p.Ile144Asn	missense_variant	3/4	1		ENSP00000483658.1
CT45A5	ENST00000487941.6	c.431T>A	p.Ile144Asn	missense_variant	4/5	2		ENSP00000427342.2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 17, 2021

The c.431T>A (p.I144N) alteration is located in exon 4 (coding exon 3) of the CT45A5 gene. This alteration results from a T to A substitution at nucleotide position 431, causing the isoleucine (I) at amino acid position 144 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	19
DANN	Benign	0.96
DEOGEN2	Benign	0.31	T;T
MetaRNN	Pathogenic	0.89	D;D
PROVEAN	Pathogenic	-6.6	D;.
Sift	Pathogenic	0.0	D;.
Sift4G	Uncertain	0.0020	D;D
Vest4		0.87
gMVP		0.11

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-134872696;