chr16-67610660-GGTT-G
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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
NM_006565.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.109
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 |
---|---|---|---|---|---|---|---|
CTCF | NM_006565.4 | c.-9-160_-9-158del | intron_variant | ENST00000264010.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTCF | ENST00000264010.10 | c.-9-160_-9-158del | intron_variant | 1 | NM_006565.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0240 AC: 3653AN: 152046Hom.: 150 Cov.: 31
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GnomAD4 exome AF: 0.00297 AC: 777AN: 261720Hom.: 22 AF XY: 0.00262 AC XY: 347AN XY: 132286
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GnomAD4 genome AF: 0.0240 AC: 3658AN: 152164Hom.: 151 Cov.: 31 AF XY: 0.0233 AC XY: 1733AN XY: 74406
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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 submitter | clinical testing | GeneDx | Jul 27, 2020 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at