dbSNP rs774932604: CT47B1:p.Glu266Lys (chrX-120874000-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001145718.3(CT47B1):c.796G>A(p.Glu266Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.00046 ( 1 hom., 2 hem., cov: 12)

Exomes 𝑓: 0.0018 ( 5 hom. 221 hem. )

Failed GnomAD Quality Control

Consequence

CT47B1
NM_001145718.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.44

Publications

2 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: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0036537647).

BP6

Variant X-120874000-C-T is Benign according to our data. Variant chrX-120874000-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2661333.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population eas. GnomAdExome4 allele frequency = 0.00182 (717/393148) while in subpopulation EAS AF = 0.0223 (526/23544). AF 95% confidence interval is 0.0208. There are 5 homozygotes in GnomAdExome4. There are 221 alleles in the male GnomAdExome4 subpopulation. Median coverage is 6. This position passed quality control check.

BS2

High Homozygotes in GnomAdExome4 at 5 gene

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.796G>A	p.Glu266Lys	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.796G>A	p.Glu266Lys	missense	Exon 2 of 3	ENSP00000360360.3	P0C2W7

Frequencies

GnomAD3 genomes

AF:

0.000461

AC:

AN:

80322

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000501

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000155

Gnomad ASJ

AF:

0.00366

Gnomad EAS

AF:

0.00831

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000185

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00201

AC:

104

AN:

51671

AF XY:

0.00201

show subpopulations

Gnomad AFR exome

AF:

0.000401

Gnomad AMR exome

AF:

0.000116

Gnomad ASJ exome

AF:

0.0114

Gnomad EAS exome

AF:

0.00927

Gnomad FIN exome

AF:

0.00153

Gnomad NFE exome

AF:

0.000558

Gnomad OTH exome

AF:

0.00182

GnomAD4 exome

AF:

0.00182

AC:

717

AN:

393148

Hom.:

Cov.:

AF XY:

0.00178

AC XY:

221

AN XY:

123970

show subpopulations

African (AFR)

AF:

0.0000925

AC:

AN:

10811

American (AMR)

AF:

0.0000683

AC:

AN:

14648

Ashkenazi Jewish (ASJ)

AF:

0.00636

AC:

AN:

10216

East Asian (EAS)

AF:

0.0223

AC:

526

AN:

23544

South Asian (SAS)

AF:

0.00120

AC:

AN:

29284

European-Finnish (FIN)

AF:

0.0000431

AC:

AN:

23223

Middle Eastern (MID)

AF:

0.000669

AC:

AN:

1495

European-Non Finnish (NFE)

AF:

0.000256

AC:

AN:

257969

Other (OTH)

AF:

0.000956

AC:

AN:

21958

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000461

AC:

AN:

80332

Hom.:

Cov.:

AF XY:

0.000160

AC XY:

AN XY:

12480

show subpopulations

African (AFR)

AF:

0.0000501

AC:

AN:

19978

American (AMR)

AF:

0.000154

AC:

AN:

6476

Ashkenazi Jewish (ASJ)

AF:

0.00366

AC:

AN:

2185

East Asian (EAS)

AF:

0.00834

AC:

AN:

2277

South Asian (SAS)

AF:

0.00

AC:

AN:

1355

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3176

Middle Eastern (MID)

AF:

0.00

AC:

AN:

149

European-Non Finnish (NFE)

AF:

0.000185

AC:

AN:

43157

Other (OTH)

AF:

0.00

AC:

AN:

1005

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

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:

0.000914

Hom.:

Bravo

AF:

0.000567

ExAC

AF:

0.00148

AC:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.51

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.072

FATHMM_MKL

Benign

0.029

LIST_S2

Benign

0.67

MetaRNN

Benign

0.0037

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.2

PhyloP100

1.4

PrimateAI

Uncertain

0.51

PROVEAN

Benign

-2.3

REVEL

Benign

0.037

Sift

Pathogenic

0.0

Sift4G

Uncertain

0.042

Polyphen

1.0

Vest4

0.037

MutPred

0.21

Gain of methylation at E266 (P = 0.0114)

MVP

0.048

MPC

0.0052

ClinPred

0.027

GERP RS

1.8

Varity_R

0.39

gMVP

0.017

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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