rs34322009

Variant names:

• chr1-214651946-CTTTTT-C
• rs34322009
• NM_016343.4:c.8160+68_8160+72delTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr1-214651946-CTTTTT-C
• chr1-214651946-CTTTTT-CT
• chr1-214651946-CTTTTT-CTT
• chr1-214651946-CTTTTT-CTTT
• chr1-214651946-CTTTTT-CTTTT
• chr1-214651946-CTTTTT-CTTTTTT
• chr1-214651946-CTTTTT-CTTTTTTT
• chr1-214651946-CTTTTT-CTTTTTTTT
• chr1-214651946-CTTTTT-CTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_016343.4(CENPF):​c.8160+68_8160+72delTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000973 in 1,027,236 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 9.7e-7 (0 hom.)
• Consequence: CENPF NM_016343.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• Stromme syndrome

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Illumina, G2P, Genomics England PanelApp

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016343.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CENPF	NM_016343.4	MANE Select	c.8160+68_8160+72delTTTTT		intron	N/A	NP_057427.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CENPF	ENST00000366955.8	TSL:1 MANE Select	c.8160+61_8160+65delTTTTT		intron	N/A	ENSP00000355922.3	P49454
	CENPF	ENST00000934982.1		c.8280+61_8280+65delTTTTT		intron	N/A	ENSP00000605041.1
	CENPF	ENST00000934983.1		c.8160+61_8160+65delTTTTT		intron	N/A	ENSP00000605042.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 9.73e-7 AC: 1 AN: 1027236 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 504144

African (AFR) AF: 0.00 AC: 0 AN: 23220

American (AMR) AF: 0.00 AC: 0 AN: 16908

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14688

East Asian (EAS) AF: 0.00 AC: 0 AN: 30134

South Asian (SAS) AF: 0.00 AC: 0 AN: 43118

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40460

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4240

European-Non Finnish (NFE) AF: 0.00000123 AC: 1 AN: 811650

Other (OTH) AF: 0.00 AC: 0 AN: 42818

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34322009; hg19: chr1-214825289;