Variant rs6025601 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001386993.1(CTCFL):c.1143T>C(p.Asp381=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,613,644 control chromosomes in the GnomAD database, including 38,820 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 0.26 ( 5588 hom., cov: 32)

Exomes 𝑓: 0.21 ( 33232 hom. )

Consequence

CTCFL
NM_001386993.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.75

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP7

Synonymous conserved (PhyloP=1.75 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTCFL	NM_001386993.1 linkuse as main transcript	c.1143T>C	p.Asp381=	synonymous_variant	6/11	ENST00000243914.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTCFL	ENST00000243914.8 linkuse as main transcript	c.1143T>C	p.Asp381=	synonymous_variant	6/11	1	NM_001386993.1	P4	Q8NI51-1

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39175

AN:

151850

Hom.:

5574

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.203

Gnomad EAS

AF:

0.374

Gnomad SAS

AF:

0.259

Gnomad FIN

AF:

0.176

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.194

Gnomad OTH

AF:

0.256

GnomAD3 exomes

AF:

0.240

AC:

60374

AN:

251408

Hom.:

7740

AF XY:

0.233

AC XY:

31673

AN XY:

135880

show subpopulations

Gnomad AFR exome

AF:

0.370

Gnomad AMR exome

AF:

0.316

Gnomad ASJ exome

AF:

0.203

Gnomad EAS exome

AF:

0.367

Gnomad SAS exome

AF:

0.239

Gnomad FIN exome

AF:

0.184

Gnomad NFE exome

AF:

0.194

Gnomad OTH exome

AF:

0.216

GnomAD4 exome

AF:

0.207

AC:

302750

AN:

1461676

Hom.:

33232

Cov.:

AF XY:

0.207

AC XY:

150619

AN XY:

727150

show subpopulations

Gnomad4 AFR exome

AF:

0.369

Gnomad4 AMR exome

AF:

0.317

Gnomad4 ASJ exome

AF:

0.199

Gnomad4 EAS exome

AF:

0.369

Gnomad4 SAS exome

AF:

0.238

Gnomad4 FIN exome

AF:

0.187

Gnomad4 NFE exome

AF:

0.190

Gnomad4 OTH exome

AF:

0.217

GnomAD4 genome

AF:

0.258

AC:

39232

AN:

151968

Hom.:

5588

Cov.:

AF XY:

0.257

AC XY:

19115

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.370

Gnomad4 AMR

AF:

0.275

Gnomad4 ASJ

AF:

0.203

Gnomad4 EAS

AF:

0.374

Gnomad4 SAS

AF:

0.258

Gnomad4 FIN

AF:

0.176

Gnomad4 NFE

AF:

0.194

Gnomad4 OTH

AF:

0.263

Alfa

AF:

0.213

Hom.:

5568

Bravo

AF:

0.272

Asia WGS

AF:

0.329

AC:

1142

AN:

3478

EpiCase

AF:

0.197

EpiControl

AF:

0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

8.7

DANN

Benign

0.50

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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