X-120874938-C-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001145718.3(CT47B1):​c.733G>T​(p.Ala245Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 22)

Consequence

CT47B1
NM_001145718.3 missense

Scores

17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0460
Variant links:
Genes affected
CT47B1 (HGNC:33293): (cancer/testis antigen family 47 member B1)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.059916645).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CT47B1NM_001145718.3 linkc.733G>T p.Ala245Ser missense_variant Exon 1 of 3 ENST00000371311.5 NP_001139190.1 P0C2W7
CT47B1XM_017029734.3 linkc.733G>T p.Ala245Ser 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.733G>T p.Ala245Ser missense_variant Exon 1 of 3 5 NM_001145718.3 ENSP00000360360.3 P0C2W7

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
22

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Mar 07, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.733G>T (p.A245S) 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 733, causing the alanine (A) at amino acid position 245 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
0.10
BayesDel_addAF
Benign
-0.46
T
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.1
DANN
Benign
0.82
DEOGEN2
Benign
0.0074
T
FATHMM_MKL
Benign
0.0078
N
LIST_S2
Benign
0.33
T
M_CAP
Benign
0.0011
T
MetaRNN
Benign
0.060
T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
1.2
L
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-0.71
N
REVEL
Benign
0.011
Sift
Benign
0.50
T
Sift4G
Benign
0.18
T
Polyphen
0.10
B
Vest4
0.075
MutPred
0.18
Gain of phosphorylation at A245 (P = 9e-04);
MVP
0.014
MPC
0.0056
ClinPred
0.033
T
GERP RS
-1.7
Varity_R
0.070
gMVP
0.0053

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-120008792; API