chr16-67610660-GGTT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006565.4(CTCF):​c.-9-160_-9-158del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 413,884 control chromosomes in the GnomAD database, including 173 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.024 ( 151 hom., cov: 31)
Exomes 𝑓: 0.0030 ( 22 hom. )

Consequence

CTCF
NM_006565.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.109
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 16-67610660-GGTT-G is Benign according to our data. Variant chr16-67610660-GGTT-G is described in ClinVar as [Benign]. Clinvar id is 1224890.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0817 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTCFNM_006565.4 linkuse as main transcriptc.-9-160_-9-158del intron_variant ENST00000264010.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTCFENST00000264010.10 linkuse as main transcriptc.-9-160_-9-158del intron_variant 1 NM_006565.4 P4P49711-1

Frequencies

GnomAD3 genomes
AF:
0.0240
AC:
3653
AN:
152046
Hom.:
150
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0841
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00767
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000622
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.0196
GnomAD4 exome
AF:
0.00297
AC:
777
AN:
261720
Hom.:
22
AF XY:
0.00262
AC XY:
347
AN XY:
132286
show subpopulations
Gnomad4 AFR exome
AF:
0.0844
Gnomad4 AMR exome
AF:
0.00497
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000264
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000130
Gnomad4 OTH exome
AF:
0.00600
GnomAD4 genome
AF:
0.0240
AC:
3658
AN:
152164
Hom.:
151
Cov.:
31
AF XY:
0.0233
AC XY:
1733
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.0840
Gnomad4 AMR
AF:
0.00766
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.0194
Alfa
AF:
0.0186
Hom.:
10
Bravo
AF:
0.0276
Asia WGS
AF:
0.00433
AC:
15
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 27, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs140708467; hg19: chr16-67644563; API