Variant rs6128059 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000243914.8(CTCFL):c.1675-33C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 1,610,770 control chromosomes in the GnomAD database, including 67,472 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.23 ( 4585 hom., cov: 32)

Exomes 𝑓: 0.29 ( 62887 hom. )

Consequence

CTCFL
ENST00000243914.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.400

Variant links:

Genes affected

CTCFL (HGNC:16234): (CCCTC-binding factor like) CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2012]

CTCFL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTCFL	NM_001386993.1 linkuse as main transcript	c.1675-33C>T		intron_variant		ENST00000243914.8	NP_001373922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTCFL	ENST00000243914.8 linkuse as main transcript	c.1675-33C>T		intron_variant		1	NM_001386993.1	ENSP00000243914	P4	Q8NI51-1

Frequencies

GnomAD3 genomes

AF:

0.228

AC:

34626

AN:

151984

Hom.:

4585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.231

GnomAD3 exomes

AF:

0.257

AC:

64096

AN:

249666

Hom.:

9087

AF XY:

0.272

AC XY:

36676

AN XY:

134980

show subpopulations

Gnomad AFR exome

AF:

0.110

Gnomad AMR exome

AF:

0.141

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.210

Gnomad SAS exome

AF:

0.377

Gnomad FIN exome

AF:

0.207

Gnomad NFE exome

AF:

0.295

Gnomad OTH exome

AF:

0.282

GnomAD4 exome

AF:

0.289

AC:

421000

AN:

1458668

Hom.:

62887

Cov.:

AF XY:

0.293

AC XY:

212595

AN XY:

725388

show subpopulations

Gnomad4 AFR exome

AF:

0.104

Gnomad4 AMR exome

AF:

0.151

Gnomad4 ASJ exome

AF:

0.262

Gnomad4 EAS exome

AF:

0.211

Gnomad4 SAS exome

AF:

0.379

Gnomad4 FIN exome

AF:

0.213

Gnomad4 NFE exome

AF:

0.300

Gnomad4 OTH exome

AF:

0.278

GnomAD4 genome

AF:

0.228

AC:

34619

AN:

152102

Hom.:

4585

Cov.:

AF XY:

0.224

AC XY:

16657

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.113

Gnomad4 AMR

AF:

0.194

Gnomad4 ASJ

AF:

0.262

Gnomad4 EAS

AF:

0.209

Gnomad4 SAS

AF:

0.354

Gnomad4 FIN

AF:

0.213

Gnomad4 NFE

AF:

0.297

Gnomad4 OTH

AF:

0.229

Alfa

AF:

0.276

Hom.:

6099

Bravo

AF:

0.220

Asia WGS

AF:

0.271

AC:

944

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.0

DANN

Benign

0.80

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over