chr1-214614108-CT-C

Variant names:

• chr1-214614108-CT-C
• rs370473275
• NM_016343.4:c.162+205delT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_016343.4(CENPF):​c.162+205delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00092 (0 hom., cov: 0)
• Consequence: CENPF NM_016343.4 intron
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000919 (113/122982) while in subpopulation SAS AF= 0.00214 (8/3734). AF 95% confidence interval is 0.00107. There are 0 homozygotes in gnomad4. There are 65 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CENPF	NM_016343.4	c.162+205delT		intron_variant	Intron 2 of 19	ENST00000366955.8	NP_057427.3
CENPF	XM_017000086.3	c.162+205delT		intron_variant	Intron 2 of 19		XP_016855575.1
CENPF	XM_011509082.4	c.162+205delT		intron_variant	Intron 2 of 18		XP_011507384.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CENPF	ENST00000366955.8	c.162+193delT		intron_variant	Intron 2 of 19	1	NM_016343.4	ENSP00000355922.3

Frequencies

GnomAD3 genomes AF: 0.000911 AC: 112 AN: 122992 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000349

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000666

Gnomad ASJ AF: 0.00129

Gnomad EAS AF: 0.000943

Gnomad SAS AF: 0.00187

Gnomad FIN AF: 0.00112

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00115

Gnomad OTH AF: 0.00179

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

GnomAD4 genome AF: 0.000919 AC: 113 AN: 122982 Hom.: 0 Cov.: 0 AF XY: 0.00111 AC XY: 65 AN XY: 58680

Gnomad4 AFR AF: 0.000349

Gnomad4 AMR AF: 0.000665

Gnomad4 ASJ AF: 0.00129

Gnomad4 EAS AF: 0.000947

Gnomad4 SAS AF: 0.00214

Gnomad4 FIN AF: 0.00112

Gnomad4 NFE AF: 0.00115

Gnomad4 OTH AF: 0.00178

ClinVar

Not reported in ClinVar

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;