X-135764291-T-C

Position:

• chrX-135764291-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001370148.2(CT45A3):​c.154A>G​(p.Met52Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 6/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: CT45A3 NM_001370148.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.95

Genes affected

CT45A3 (HGNC:33268): (cancer/testis antigen family 45 member A3) Predicted to be involved in snRNA 3'-end processing. Predicted to be part of integrator complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.05234003).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CT45A3	NM_001370148.2	c.154A>G	p.Met52Val	missense_variant	2/5	ENST00000598716.3	NP_001357077.1
CT45A3	NM_001017435.2	c.154A>G	p.Met52Val	missense_variant	2/5		NP_001017435.1
CT45A3	NM_001370149.1	c.154A>G	p.Met52Val	missense_variant	2/5		NP_001357078.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CT45A3	ENST00000598716.3	c.154A>G	p.Met52Val	missense_variant	2/5	3	NM_001370148.2	ENSP00000471571	P1
CT45A3	ENST00000597510.6	c.154A>G	p.Met52Val	missense_variant	1/4	1		ENSP00000471418	P1

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

Feb 28, 2024

The c.154A>G (p.M52V) alteration is located in exon 2 (coding exon 1) of the CT45A3 gene. This alteration results from a A to G substitution at nucleotide position 154, causing the methionine (M) at amino acid position 52 to be replaced by a valine (V). 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
AlphaMissense	Benign	0.088
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.45
DANN	Benign	0.32
DEOGEN2	Benign	0.0094	T;T
LIST_S2	Benign	0.52	T;.
MetaRNN	Benign	0.052	T;T
Sift4G	Benign	0.66	T;T
Vest4		0.064
gMVP		0.028

Splicing

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-134887386;