X-120874974-C-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_001145718.3(CT47B1):​c.697G>C​(p.Glu233Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000538 in 1,208,975 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000036 ( 0 hom., 2 hem., cov: 22)
Exomes 𝑓: 0.000056 ( 0 hom. 17 hem. )

Consequence

CT47B1
NM_001145718.3 missense

Scores

3
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.22
Variant links:
Genes affected
CT47B1 (HGNC:33293): (cancer/testis antigen family 47 member B1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.13370389).
BS2
High Hemizygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CT47B1NM_001145718.3 linkc.697G>C p.Glu233Gln missense_variant Exon 1 of 3 ENST00000371311.5 NP_001139190.1 P0C2W7
CT47B1XM_017029734.3 linkc.697G>C p.Glu233Gln missense_variant Exon 1 of 3 XP_016885223.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CT47B1ENST00000371311.5 linkc.697G>C p.Glu233Gln missense_variant Exon 1 of 3 5 NM_001145718.3 ENSP00000360360.3 P0C2W7

Frequencies

GnomAD3 genomes
AF:
0.0000355
AC:
4
AN:
112653
Hom.:
0
Cov.:
22
AF XY:
0.0000574
AC XY:
2
AN XY:
34825
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.0000752
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000438
AC:
8
AN:
182615
Hom.:
0
AF XY:
0.0000444
AC XY:
3
AN XY:
67569
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.0000860
Gnomad OTH exome
AF:
0.000222
GnomAD4 exome
AF:
0.0000556
AC:
61
AN:
1096322
Hom.:
0
Cov.:
31
AF XY:
0.0000469
AC XY:
17
AN XY:
362306
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000185
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000666
Gnomad4 OTH exome
AF:
0.0000870
GnomAD4 genome
AF:
0.0000355
AC:
4
AN:
112653
Hom.:
0
Cov.:
22
AF XY:
0.0000574
AC XY:
2
AN XY:
34825
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000752
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000142
Hom.:
1
Bravo
AF:
0.0000264
ExAC
AF:
0.0000496
AC:
6
EpiCase
AF:
0.000109
EpiControl
AF:
0.000119

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Jun 17, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.697G>C (p.E233Q) alteration is located in exon 1 (coding exon 1) of the CT47B1 gene. This alteration results from a G to C substitution at nucleotide position 697, causing the glutamic acid (E) at amino acid position 233 to be replaced by a glutamine (Q). 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
0.15
BayesDel_addAF
Benign
-0.56
T
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.1
DANN
Benign
0.83
DEOGEN2
Benign
0.039
T
FATHMM_MKL
Benign
0.015
N
LIST_S2
Benign
0.35
T
M_CAP
Benign
0.00098
T
MetaRNN
Benign
0.13
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.1
M
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-1.4
N
REVEL
Benign
0.067
Sift
Uncertain
0.028
D
Sift4G
Benign
0.075
T
Polyphen
0.94
P
Vest4
0.051
MVP
0.014
MPC
0.0055
ClinPred
0.043
T
GERP RS
1.4
Varity_R
0.090
gMVP
0.021

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

LitVar

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

Other links and lift over

dbSNP: rs757090872; hg19: chrX-120008828; API