rs782624081

Variant names:

• chrX-135158282-C-G
• rs782624081
• NM_001031705.3:c.454G>C

Your query was ambiguous. Multiple possible variants found:

• chrX-135158282-C-G
• chrX-135158282-C-T

Variant summary

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

The NM_001031705.3(CT55):​c.454G>C​(p.Glu152Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000916 in 1,091,696 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E152K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 9.2e-7 (0 hom. 0 hem.)
• Consequence: CT55 NM_001031705.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 0 publications found

Genes affected

CT55 (HGNC:26047): (cancer/testis antigen 55)

CT55 Gene-Disease associations (from GenCC):

• spermatogenic failure, X-linked, 7

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

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=0.11241746).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CT55	NM_001031705.3	c.454G>C	p.Glu152Gln	missense_variant	Exon 4 of 6	ENST00000276241.11	NP_001026875.1
CT55	NM_017863.2	c.454G>C	p.Glu152Gln	missense_variant	Exon 4 of 5		NP_060333.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CT55	ENST00000276241.11	c.454G>C	p.Glu152Gln	missense_variant	Exon 4 of 6	1	NM_001031705.3	ENSP00000276241.6
CT55	ENST00000344129.2	c.454G>C	p.Glu152Gln	missense_variant	Exon 4 of 5	1		ENSP00000343893.2

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome AF: 9.16e-7 AC: 1 AN: 1091696 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 357274

African (AFR) AF: 0.00 AC: 0 AN: 26289

American (AMR) AF: 0.00 AC: 0 AN: 35174

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19331

East Asian (EAS) AF: 0.00 AC: 0 AN: 30163

South Asian (SAS) AF: 0.00 AC: 0 AN: 53917

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40485

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4117

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 836382

Other (OTH) AF: 0.0000218 AC: 1 AN: 45838

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.8
DANN	Benign	0.72
DEOGEN2	Benign	0.045	T;.
FATHMM_MKL	Benign	0.10	N
LIST_S2	Benign	0.39	T;T
M_CAP	Benign	0.0027	T
MetaRNN	Benign	0.11	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.4	L;L
PhyloP100		1.1
PROVEAN	Benign	-1.7	N;N
REVEL	Benign	0.051
Sift	Benign	0.16	T;T
Sift4G	Benign	0.094	T;T
Polyphen		0.77	P;.
Vest4		0.15
MutPred		0.40		Loss of ubiquitination at K147 (P = 0.0755);Loss of ubiquitination at K147 (P = 0.0755);
MVP		0.043
MPC		0.37
ClinPred		0.25	T
GERP RS		1.3
Varity_R		0.11
gMVP		0.11
Mutation Taster		=97/3	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

dbSNP: rs782624081; hg19: chrX-134292207;