rs111512847

Variant names:

• chr1-214614087-A-C
• rs111512847
• NM_016343.4:c.162+171A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-214614087-A-C
• chr1-214614087-A-G
• chr1-214614087-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_016343.4(CENPF):​c.162+171A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.057 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: CENPF NM_016343.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CENPF	NM_016343.4	c.162+171A>C		intron_variant	Intron 2 of 19	ENST00000366955.8	NP_057427.3
CENPF	XM_017000086.3	c.162+171A>C		intron_variant	Intron 2 of 19		XP_016855575.1
CENPF	XM_011509082.4	c.162+171A>C		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+171A>C		intron_variant	Intron 2 of 19	1	NM_016343.4	ENSP00000355922.3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2479 AN: 43664 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.0278

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0235

Gnomad MID AF: 0.0366

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.0635

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0568 AC: 2481 AN: 43694 Hom.: 0 Cov.: 0 AF XY: 0.0532 AC XY: 1120 AN XY: 21058

Gnomad4 AFR AF: 0.0631

Gnomad4 AMR AF: 0.0292

Gnomad4 ASJ AF: 0.0642

Gnomad4 EAS AF: 0.0256

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.0235

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.0627

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.060

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: rs111512847; hg19: chr1-214787430; COSMIC: COSV65274469; COSMIC: COSV65274469;