Variant chr1-214613787-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The ENST00000366955.8(CENPF):c.33G>A(p.Gly11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,607,980 control chromosomes in the GnomAD database, including 189,616 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 12687 hom., cov: 32)

Exomes 𝑓: 0.48 ( 176929 hom. )

Consequence

CENPF
ENST00000366955.8 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.213

Variant links:

Genes affected

CENPF (HGNC:1857): (centromere protein F) This gene encodes a protein that associates with the centromere-kinetochore complex. The protein is a component of the nuclear matrix during the G2 phase of interphase. In late G2 the protein associates with the kinetochore and maintains this association through early anaphase. It localizes to the spindle midzone and the intracellular bridge in late anaphase and telophase, respectively, and is thought to be subsequently degraded. The localization of this protein suggests that it may play a role in chromosome segregation during mitotis. It is thought to form either a homodimer or heterodimer. Autoantibodies against this protein have been found in patients with cancer or graft versus host disease. [provided by RefSeq, Jul 2008]

CENPF links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 1-214613787-G-A is Benign according to our data. Variant chr1-214613787-G-A is described in ClinVar as [Benign]. Clinvar id is 1209807.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.213 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CENPF	NM_016343.4 linkuse as main transcript	c.33G>A	p.Gly11=	synonymous_variant	2/20	ENST00000366955.8	NP_057427.3
CENPF	XM_017000086.3 linkuse as main transcript	c.33G>A	p.Gly11=	synonymous_variant	2/20		XP_016855575.1
CENPF	XM_011509082.4 linkuse as main transcript	c.33G>A	p.Gly11=	synonymous_variant	2/19		XP_011507384.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CENPF	ENST00000366955.8 linkuse as main transcript	c.33G>A	p.Gly11=	synonymous_variant	2/20	1	NM_016343.4	ENSP00000355922	P2

Frequencies

GnomAD3 genomes

AF:

0.364

AC:

55368

AN:

151948

Hom.:

12688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.552

Gnomad AMR

AF:

0.330

Gnomad ASJ

AF:

0.496

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.459

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.526

Gnomad OTH

AF:

0.382

GnomAD3 exomes

AF:

0.397

AC:

97610

AN:

245878

Hom.:

22388

AF XY:

0.409

AC XY:

54355

AN XY:

132988

show subpopulations

Gnomad AFR exome

AF:

0.0981

Gnomad AMR exome

AF:

0.262

Gnomad ASJ exome

AF:

0.494

Gnomad EAS exome

AF:

0.117

Gnomad SAS exome

AF:

0.325

Gnomad FIN exome

AF:

0.463

Gnomad NFE exome

AF:

0.520

Gnomad OTH exome

AF:

0.434

GnomAD4 exome

AF:

0.480

AC:

698572

AN:

1455914

Hom.:

176929

Cov.:

AF XY:

0.477

AC XY:

345750

AN XY:

724178

show subpopulations

Gnomad4 AFR exome

AF:

0.0906

Gnomad4 AMR exome

AF:

0.269

Gnomad4 ASJ exome

AF:

0.493

Gnomad4 EAS exome

AF:

0.130

Gnomad4 SAS exome

AF:

0.326

Gnomad4 FIN exome

AF:

0.459

Gnomad4 NFE exome

AF:

0.527

Gnomad4 OTH exome

AF:

0.446

GnomAD4 genome

AF:

0.364

AC:

55368

AN:

152066

Hom.:

12687

Cov.:

AF XY:

0.359

AC XY:

26663

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.109

Gnomad4 AMR

AF:

0.329

Gnomad4 ASJ

AF:

0.496

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.309

Gnomad4 FIN

AF:

0.459

Gnomad4 NFE

AF:

0.526

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.464

Hom.:

13006

Bravo

AF:

0.342

Asia WGS

AF:

0.197

AC:

689

AN:

3478

EpiCase

AF:

0.521

EpiControl

AF:

0.510

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 07, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Stromme syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

8.9

DANN

Benign

0.83

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over