chr1-214651946-CT-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BS1
The NM_016343.4(CENPF):c.8160+72delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,046,196 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: 𝑓 0.0013 ( 0 hom., cov: 27)
Exomes 𝑓: 0.14 ( 0 hom. )
Consequence
CENPF
NM_016343.4 intron
NM_016343.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.169
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Variant has high frequency in the EAS (0.261) population. However there is too low homozygotes in high coverage region: (expected more than 4076, got 0).
BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00132 (186/140446) while in subpopulation EAS AF = 0.00185 (9/4868). AF 95% confidence interval is 0.00122. There are 0 homozygotes in GnomAd4. There are 90 alleles in the male GnomAd4 subpopulation. Median coverage is 27. This position passed quality control check.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CENPF | NM_016343.4 | c.8160+72delT | intron_variant | Intron 15 of 19 | ENST00000366955.8 | NP_057427.3 | ||
| CENPF | XM_017000086.3 | c.8160+72delT | intron_variant | Intron 15 of 19 | XP_016855575.1 | |||
| CENPF | XM_011509082.4 | c.7984-870delT | 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+61delT | intron_variant | Intron 15 of 19 | 1 | NM_016343.4 | ENSP00000355922.3 | |||
| CENPF | ENST00000706765.1 | c.7984-881delT | intron_variant | Intron 14 of 18 | ENSP00000516538.1 | |||||
| CENPF | ENST00000467765.1 | n.330+61delT | intron_variant | Intron 2 of 3 | 2 |
Frequencies
GnomAD3 genomes 0.00130 AC: 183AN: 140428Hom.: 0 Cov.: 27 show subpopulations
GnomAD3 genomes
AF:
AC:
183
AN:
140428
Hom.:
Cov.:
27
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.144 AC: 130418AN: 905750Hom.: 0 AF XY: 0.148 AC XY: 65792AN XY: 443322 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
130418
AN:
905750
Hom.:
AF XY:
AC XY:
65792
AN XY:
443322
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1408
AN:
21836
American (AMR)
AF:
AC:
2875
AN:
14712
Ashkenazi Jewish (ASJ)
AF:
AC:
2239
AN:
12168
East Asian (EAS)
AF:
AC:
5960
AN:
22354
South Asian (SAS)
AF:
AC:
6791
AN:
39462
European-Finnish (FIN)
AF:
AC:
6394
AN:
29498
Middle Eastern (MID)
AF:
AC:
351
AN:
3712
European-Non Finnish (NFE)
AF:
AC:
98611
AN:
724498
Other (OTH)
AF:
AC:
5789
AN:
37510
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.274
Heterozygous variant carriers
0
12349
24698
37047
49396
61745
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00132 AC: 186AN: 140446Hom.: 0 Cov.: 27 AF XY: 0.00133 AC XY: 90AN XY: 67890 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
186
AN:
140446
Hom.:
Cov.:
27
AF XY:
AC XY:
90
AN XY:
67890
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
60
AN:
39108
American (AMR)
AF:
AC:
9
AN:
13950
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3312
East Asian (EAS)
AF:
AC:
9
AN:
4868
South Asian (SAS)
AF:
AC:
2
AN:
4394
European-Finnish (FIN)
AF:
AC:
42
AN:
7630
Middle Eastern (MID)
AF:
AC:
0
AN:
262
European-Non Finnish (NFE)
AF:
AC:
61
AN:
64106
Other (OTH)
AF:
AC:
3
AN:
1924
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.348
Heterozygous variant carriers
0
15
30
44
59
74
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at