NM_001007551.6:c.455A>G

Variant names:

• chrX-135778975-T-C
• NM_001007551.6:c.455A>G

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_001007551.6(CT45A5):​c.455A>G​(p.Gln152Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign 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: 2.29
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.38221943).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001007551.6. 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
	CT45A5	NM_001007551.6	MANE Select	c.455A>G	p.Gln152Arg	missense	Exon 4 of 5	NP_001007552.2	P0DMU8
	CT45A5	NM_001172288.2		c.455A>G	p.Gln152Arg	missense	Exon 4 of 5	NP_001165759.2	P0DMU8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CT45A5	ENST00000698999.1	MANE Select	c.455A>G	p.Gln152Arg	missense	Exon 4 of 5	ENSP00000514077.1	P0DMU8
	CT45A5	ENST00000617203.1	TSL:1	c.455A>G	p.Gln152Arg	missense	Exon 3 of 4	ENSP00000483658.1	P0DMU8
	CT45A5	ENST00000487941.6	TSL:2	c.455A>G	p.Gln152Arg	missense	Exon 4 of 5	ENSP00000427342.2	P0DMU8

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

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
BayesDel_noAF	Benign	-0.43
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.24	T
MetaRNN	Benign	0.38	T
PhyloP100		2.3
PROVEAN	Uncertain	-3.7	D
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Vest4		0.28
gMVP		0.0048

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-134872720;