1-214614108-C-CTT

Variant summary

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

The NM_016343.4(CENPF):c.162+204_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 0.027 (188 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-CTT is Benign according to our data. Variant chr1-214614108-C-CTT is described in ClinVar as [Benign]. Clinvar id is 1183371.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CENPF	NM_016343.4	c.162+204_162+205dup		intron_variant		ENST00000366955.8
CENPF	XM_011509082.4	c.162+204_162+205dup		intron_variant
CENPF	XM_017000086.3	c.162+204_162+205dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CENPF	ENST00000366955.8	c.162+204_162+205dup		intron_variant		1	NM_016343.4	P2
CENPF	ENST00000706765.1	c.162+204_162+205dup		intron_variant				A2
CENPF	ENST00000464322.5	n.330+204_330+205dup		intron_variant, non_coding_transcript_variant		2
CENPF	ENST00000706764.1	n.340+204_340+205dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 3343 AN: 123024 Hom.: 188 Cov.: 0

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0122

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000236

Gnomad SAS AF: 0.000533

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00370

Gnomad NFE AF: 0.000505

Gnomad OTH AF: 0.0155

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

GnomAD4 genome AF: 0.0272 AC: 3346 AN: 123014 Hom.: 188 Cov.: 0 AF XY: 0.0250 AC XY: 1470 AN XY: 58696

Gnomad4 AFR AF: 0.0996

Gnomad4 AMR AF: 0.0122

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000237

Gnomad4 SAS AF: 0.000536

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000505

Gnomad4 OTH AF: 0.0154

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

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Computational scores

Source: dbNSFP v4.3

Splicing

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;