chr1-214651889-GAAA-TTTGT

Variant names:

• chr1-214651889-GAAA-TTTGT
• NM_016343.4:c.8160+3_8160+6delGAAAinsTTTGT

Variant summary

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

The NM_016343.4(CENPF):​c.8160+3_8160+6delGAAAinsTTTGT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CENPF NM_016343.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28

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

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CENPF	NM_016343.4	c.8160+3_8160+6delGAAAinsTTTGT		splice_region_variant, intron_variant	Intron 15 of 19	ENST00000366955.8	NP_057427.3
CENPF	XM_017000086.3	c.8160+3_8160+6delGAAAinsTTTGT		splice_region_variant, intron_variant	Intron 15 of 19		XP_016855575.1
CENPF	XM_011509082.4	c.7984-939_7984-936delGAAAinsTTTGT		intron_variant	Intron 14 of 18		XP_011507384.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CENPF	ENST00000366955.8	c.8160+3_8160+6delGAAAinsTTTGT		splice_region_variant, intron_variant	Intron 15 of 19	1	NM_016343.4	ENSP00000355922.3
CENPF	ENST00000706765.1	c.7984-939_7984-936delGAAAinsTTTGT		intron_variant	Intron 14 of 18			ENSP00000516538.1
CENPF	ENST00000467765.1	n.330+3_330+6delGAAAinsTTTGT		splice_region_variant, intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-214825232;