chrX-135160525-C-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001031705.3(CT55):​c.310G>T​(p.Ala104Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000344 in 1,192,722 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.000036 ( 0 hom. 11 hem. )

Consequence

CT55
NM_001031705.3 missense

Scores

16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.898
Variant links:
Genes affected
CT55 (HGNC:26047): (cancer/testis antigen 55)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.011258483).
BS2
High Hemizygotes in GnomAdExome4 at 11 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CT55NM_001031705.3 linkc.310G>T p.Ala104Ser missense_variant Exon 3 of 6 ENST00000276241.11 NP_001026875.1 Q8WUE5-1
CT55NM_017863.2 linkc.310G>T p.Ala104Ser missense_variant Exon 3 of 5 NP_060333.1 Q8WUE5-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CT55ENST00000276241.11 linkc.310G>T p.Ala104Ser missense_variant Exon 3 of 6 1 NM_001031705.3 ENSP00000276241.6 Q8WUE5-1
CT55ENST00000344129.2 linkc.310G>T p.Ala104Ser missense_variant Exon 3 of 5 1 ENSP00000343893.2 Q8WUE5-2

Frequencies

GnomAD3 genomes
AF:
0.0000179
AC:
2
AN:
111912
Hom.:
0
Cov.:
22
AF XY:
0.00
AC XY:
0
AN XY:
34108
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000190
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000195
AC:
32
AN:
163916
Hom.:
0
AF XY:
0.000189
AC XY:
10
AN XY:
52900
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00142
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000361
AC:
39
AN:
1080810
Hom.:
0
Cov.:
29
AF XY:
0.0000313
AC XY:
11
AN XY:
351310
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00121
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000221
GnomAD4 genome
AF:
0.0000179
AC:
2
AN:
111912
Hom.:
0
Cov.:
22
AF XY:
0.00
AC XY:
0
AN XY:
34108
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000190
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000529
ExAC
AF:
0.000214
AC:
26

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 03, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.310G>T (p.A104S) alteration is located in exon 3 (coding exon 3) of the CT55 gene. This alteration results from a G to T substitution at nucleotide position 310, causing the alanine (A) at amino acid position 104 to be replaced by a serine (S). 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
0.082
BayesDel_addAF
Benign
-0.81
T
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.015
DANN
Benign
0.19
DEOGEN2
Benign
0.0030
T;.
FATHMM_MKL
Benign
0.0048
N
LIST_S2
Benign
0.26
T;T
M_CAP
Benign
0.0033
T
MetaRNN
Benign
0.011
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.34
N;N
PROVEAN
Benign
0.72
N;N
REVEL
Benign
0.020
Sift
Benign
0.75
T;T
Sift4G
Benign
0.73
T;T
Polyphen
0.43
B;.
Vest4
0.057
MutPred
0.25
Gain of glycosylation at A104 (P = 0.0053);Gain of glycosylation at A104 (P = 0.0053);
MVP
0.043
MPC
0.17
ClinPred
0.029
T
GERP RS
-1.1
Varity_R
0.042
gMVP
0.053

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs782034926; hg19: chrX-134294450; API