1-214614108-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_016343.4(CENPF):c.162+205dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (2087 hom., cov: 0)
• Consequence: CENPF NM_016343.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.288

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-214614108-C-CT is Benign according to our data. Variant chr1-214614108-C-CT is described in ClinVar as [Benign]. Clinvar id is 1249271.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CENPF	NM_016343.4	c.162+205dup		intron_variant		ENST00000366955.8
CENPF	XM_011509082.4	c.162+205dup		intron_variant
CENPF	XM_017000086.3	c.162+205dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CENPF	ENST00000366955.8	c.162+205dup		intron_variant		1	NM_016343.4	P2
CENPF	ENST00000706765.1	c.162+205dup		intron_variant				A2
CENPF	ENST00000464322.5	n.330+205dup		intron_variant, non_coding_transcript_variant		2
CENPF	ENST00000706764.1	n.340+205dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.133 AC: 16372 AN: 122984 Hom.: 2080 Cov.: 0

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.0445

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0647

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.0926

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.115

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.133 AC: 16389 AN: 122974 Hom.: 2087 Cov.: 0 AF XY: 0.133 AC XY: 7811 AN XY: 58684

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0647

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0265

Gnomad4 NFE AF: 0.0482

Gnomad4 OTH AF: 0.115

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs370473275; hg19: chr1-214787451;