Variant 16-67637901-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006565.4(CTCF):c.*29T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.098 in 1,552,148 control chromosomes in the GnomAD database, including 10,100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2698 hom., cov: 32)

Exomes 𝑓: 0.092 ( 7402 hom. )

Consequence

CTCF
NM_006565.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.500

Variant links:

Genes affected

CTCF (HGNC:13723): (CCCTC-binding factor) This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. Depending upon the context of the site, the protein can bind a histone acetyltransferase (HAT)-containing complex and function as a transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as a transcriptional repressor. If the protein is bound to a transcriptional insulator element, it can block communication between enhancers and upstream promoters, thereby regulating imprinted expression. Mutations in this gene have been associated with invasive breast cancers, prostate cancers, and Wilms' tumors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

CTCF links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 16-67637901-T-G is Benign according to our data. Variant chr16-67637901-T-G is described in ClinVar as [Benign]. Clinvar id is 1244031.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTCF	NM_006565.4 link	c.*29T>G		3_prime_UTR_variant	Exon 12 of 12	ENST00000264010.10	NP_006556.1	P49711-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTCF	ENST00000264010.10 link	c.*29T>G		3_prime_UTR_variant	Exon 12 of 12	1	NM_006565.4	ENSP00000264010.4		P49711-1

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22805

AN:

152094

Hom.:

2672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.323

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.0829

Gnomad ASJ

AF:

0.0467

Gnomad EAS

AF:

0.0131

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0841

Gnomad OTH

AF:

0.125

GnomAD3 exomes

AF:

0.103

AC:

23287

AN:

225612

Hom.:

1729

AF XY:

0.100

AC XY:

12330

AN XY:

122994

show subpopulations

Gnomad AFR exome

AF:

0.327

Gnomad AMR exome

AF:

0.0551

Gnomad ASJ exome

AF:

0.0539

Gnomad EAS exome

AF:

0.0128

Gnomad SAS exome

AF:

0.130

Gnomad FIN exome

AF:

0.124

Gnomad NFE exome

AF:

0.0897

Gnomad OTH exome

AF:

0.0884

GnomAD4 exome

AF:

0.0923

AC:

129163

AN:

1399936

Hom.:

7402

Cov.:

AF XY:

0.0925

AC XY:

64067

AN XY:

692944

show subpopulations

Gnomad4 AFR exome

AF:

0.348

Gnomad4 AMR exome

AF:

0.0559

Gnomad4 ASJ exome

AF:

0.0504

Gnomad4 EAS exome

AF:

0.0121

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.122

Gnomad4 NFE exome

AF:

0.0863

Gnomad4 OTH exome

AF:

0.0949

GnomAD4 genome

AF:

0.150

AC:

22883

AN:

152212

Hom.:

2698

Cov.:

AF XY:

0.149

AC XY:

11077

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.324

Gnomad4 AMR

AF:

0.0826

Gnomad4 ASJ

AF:

0.0467

Gnomad4 EAS

AF:

0.0133

Gnomad4 SAS

AF:

0.111

Gnomad4 FIN

AF:

0.126

Gnomad4 NFE

AF:

0.0841

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.0849

Hom.:

1280

Bravo

AF:

0.153

Asia WGS

AF:

0.105

AC:

368

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 03, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

3.9

DANN

Benign

0.64

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over