X-120874977-C-A

Variant summary

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

The NM_001145718.3(CT47B1):​c.694G>T​(p.Ala232Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000314 in 1,208,900 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A232T) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000044 ( 0 hom., 2 hem., cov: 22)
Exomes 𝑓: 0.000030 ( 0 hom. 14 hem. )

Consequence

CT47B1
NM_001145718.3 missense

Scores

1
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.09
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 Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.038754046).
BS2
High Hemizygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CT47B1NM_001145718.3 linkc.694G>T p.Ala232Ser missense_variant Exon 1 of 3 ENST00000371311.5 NP_001139190.1 P0C2W7
CT47B1XM_017029734.3 linkc.694G>T p.Ala232Ser 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.694G>T p.Ala232Ser missense_variant Exon 1 of 3 5 NM_001145718.3 ENSP00000360360.3 P0C2W7

Frequencies

GnomAD3 genomes
AF:
0.0000444
AC:
5
AN:
112587
Hom.:
0
Cov.:
22
AF XY:
0.0000575
AC XY:
2
AN XY:
34775
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000186
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:
0.0000564
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000329
AC:
6
AN:
182585
Hom.:
0
AF XY:
0.0000592
AC XY:
4
AN XY:
67553
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000729
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000525
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000369
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000301
AC:
33
AN:
1096313
Hom.:
0
Cov.:
31
AF XY:
0.0000386
AC XY:
14
AN XY:
362289
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000852
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:
0.0000333
Gnomad4 OTH exome
AF:
0.0000217
GnomAD4 genome
AF:
0.0000444
AC:
5
AN:
112587
Hom.:
0
Cov.:
22
AF XY:
0.0000575
AC XY:
2
AN XY:
34775
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000186
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000564
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000567
ExAC
AF:
0.0000414
AC:
5

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.694G>T (p.A232S) alteration is located in exon 1 (coding exon 1) of the CT47B1 gene. This alteration results from a G to T substitution at nucleotide position 694, causing the alanine (A) at amino acid position 232 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
0.096
BayesDel_addAF
Benign
-0.63
T
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.36
DANN
Benign
0.83
DEOGEN2
Benign
0.012
T
FATHMM_MKL
Benign
0.0015
N
LIST_S2
Benign
0.30
T
M_CAP
Benign
0.0032
T
MetaRNN
Benign
0.039
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.90
L
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-0.93
N
REVEL
Benign
0.011
Sift
Benign
0.73
T
Sift4G
Benign
0.083
T
Polyphen
0.090
B
Vest4
0.031
MVP
0.014
MPC
0.0056
ClinPred
0.022
T
GERP RS
-2.9
Varity_R
0.058
gMVP
0.0089

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: rs953754332; hg19: chrX-120008831; API