X-135764407-T-G

Position:

• chrX-135764407-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001370148.2(CT45A3):​c.38A>C​(p.Glu13Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/10 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: 1.16

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 -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.09334555).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CT45A3	NM_001370148.2	c.38A>C	p.Glu13Ala	missense_variant	2/5	ENST00000598716.3	NP_001357077.1
CT45A3	NM_001017435.2	c.38A>C	p.Glu13Ala	missense_variant	2/5		NP_001017435.1
CT45A3	NM_001370149.1	c.38A>C	p.Glu13Ala	missense_variant	2/5		NP_001357078.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CT45A3	ENST00000598716.3	c.38A>C	p.Glu13Ala	missense_variant	2/5	3	NM_001370148.2	ENSP00000471571	P1
CT45A3	ENST00000597510.6	c.38A>C	p.Glu13Ala	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 03, 2022

The c.38A>C (p.E13A) alteration is located in exon 2 (coding exon 1) of the CT45A3 gene. This alteration results from a A to C substitution at nucleotide position 38, causing the glutamic acid (E) at amino acid position 13 to be replaced by an alanine (A). 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	0.19
BayesDel_noAF	Benign	-0.64
CADD	Benign	19
DANN	Benign	0.96
DEOGEN2	Benign	0.032	T;T
LIST_S2	Benign	0.54	T;.
MetaRNN	Benign	0.093	T;T
Sift4G	Uncertain	0.021	D;D
Vest4		0.085
gMVP		0.026

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-134887270;