dbSNP rs774173039: CT47B1:p.Ser296Tyr (chrX-120873909-G-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001145718.3(CT47B1):c.887C>A(p.Ser296Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000012 ( 0 hom., 0 hem., cov: 12)

Exomes 𝑓: 0.0000074 ( 0 hom. 2 hem. )

Failed GnomAD Quality Control

Consequence

CT47B1
NM_001145718.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -2.16

Publications

0 publications found

Variant links:

Genes affected

CT47B1 (HGNC:33293): (cancer/testis antigen family 47 member B1)

CT47B1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.06378287).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145718.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CT47B1	NM_001145718.3	MANE Select	c.887C>A	p.Ser296Tyr	missense	Exon 2 of 3	NP_001139190.1	P0C2W7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CT47B1	ENST00000371311.5	TSL:5 MANE Select	c.887C>A	p.Ser296Tyr	missense	Exon 2 of 3	ENSP00000360360.3	P0C2W7

Frequencies

GnomAD3 genomes

AF:

0.0000125

AC:

AN:

80040

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000147

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

GnomAD2 exomes

AF:

0.00000581

AC:

AN:

171982

AF XY:

0.0000158

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000369

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000743

AC:

AN:

1077295

Hom.:

Cov.:

AF XY:

0.00000568

AC XY:

AN XY:

352147

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26155

American (AMR)

AF:

0.000200

AC:

AN:

34952

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18993

East Asian (EAS)

AF:

0.00

AC:

AN:

29881

South Asian (SAS)

AF:

0.00

AC:

AN:

53899

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29000

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3121

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

835860

Other (OTH)

AF:

0.0000220

AC:

AN:

45434

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000125

AC:

AN:

80051

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

14915

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

19017

American (AMR)

AF:

0.000147

AC:

AN:

6796

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2201

East Asian (EAS)

AF:

0.00

AC:

AN:

2717

South Asian (SAS)

AF:

0.00

AC:

AN:

1636

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3451

Middle Eastern (MID)

AF:

0.00

AC:

AN:

158

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

42463

Other (OTH)

AF:

0.00

AC:

AN:

1048

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ExAC

AF:

0.0000168

AC:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.31

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.3

(source)

DANN

Benign

0.77

DEOGEN2

Benign

0.078

FATHMM_MKL

Benign

0.0020

LIST_S2

Benign

0.54

M_CAP

Benign

0.0012

MetaRNN

Benign

0.064

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.81

PhyloP100

-2.2

PrimateAI

Benign

0.30

PROVEAN

Uncertain

-3.3

REVEL

Benign

0.035

Sift

Uncertain

0.0050

Sift4G

Uncertain

0.036

Polyphen

0.80

Vest4

0.11

MutPred

0.18

Gain of helix (P = 0.0325)

MVP

0.014

MPC

0.0049

ClinPred

0.16

GERP RS

-1.6

Varity_R

0.14

gMVP

0.0028

Mutation Taster

=100/0

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over