17-78892237-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001243540.2(CEP295NL):c.267C>T(p.Gly89Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00764 in 1,550,974 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0057 ( 9 hom., cov: 33)
Exomes 𝑓: 0.0078 ( 55 hom. )
Consequence
CEP295NL
NM_001243540.2 synonymous
NM_001243540.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.34
Publications
1 publications found
Genes affected
CEP295NL (HGNC:44659): (CEP295 N-terminal like) Predicted to enable microtubule binding activity. Predicted to be involved in regulation of centriole replication. Predicted to be located in motile cilium. Predicted to be active in centriole; centrosome; and cytosol. [provided by Alliance of Genome Resources, Apr 2022]
TIMP2 (HGNC:11821): (TIMP metallopeptidase inhibitor 2) This gene is a member of the TIMP gene family. The proteins encoded by this gene family are natural inhibitors of the matrix metalloproteinases, a group of peptidases involved in degradation of the extracellular matrix. In addition to an inhibitory role against metalloproteinases, the encoded protein has a unique role among TIMP family members in its ability to directly suppress the proliferation of endothelial cells. As a result, the encoded protein may be critical to the maintenance of tissue homeostasis by suppressing the proliferation of quiescent tissues in response to angiogenic factors, and by inhibiting protease activity in tissues undergoing remodelling of the extracellular matrix. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 17-78892237-G-A is Benign according to our data. Variant chr17-78892237-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2648382.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.34 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP295NL | NM_001243540.2 | c.267C>T | p.Gly89Gly | synonymous_variant | Exon 3 of 3 | ENST00000322630.3 | NP_001230469.1 | |
TIMP2 | NM_003255.5 | c.131-18318C>T | intron_variant | Intron 1 of 4 | ENST00000262768.11 | NP_003246.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP295NL | ENST00000322630.3 | c.267C>T | p.Gly89Gly | synonymous_variant | Exon 3 of 3 | 2 | NM_001243540.2 | ENSP00000312767.2 | ||
TIMP2 | ENST00000262768.11 | c.131-18318C>T | intron_variant | Intron 1 of 4 | 1 | NM_003255.5 | ENSP00000262768.6 |
Frequencies
GnomAD3 genomes AF: 0.00572 AC: 870AN: 152216Hom.: 9 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
870
AN:
152216
Hom.:
Cov.:
33
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:
GnomAD2 exomes AF: 0.00572 AC: 859AN: 150226 AF XY: 0.00549 show subpopulations
GnomAD2 exomes
AF:
AC:
859
AN:
150226
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
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Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00785 AC: 10979AN: 1398640Hom.: 55 Cov.: 31 AF XY: 0.00760 AC XY: 5240AN XY: 689830 show subpopulations
GnomAD4 exome
AF:
AC:
10979
AN:
1398640
Hom.:
Cov.:
31
AF XY:
AC XY:
5240
AN XY:
689830
show subpopulations
African (AFR)
AF:
AC:
48
AN:
31600
American (AMR)
AF:
AC:
32
AN:
35704
Ashkenazi Jewish (ASJ)
AF:
AC:
2
AN:
25182
East Asian (EAS)
AF:
AC:
2
AN:
35740
South Asian (SAS)
AF:
AC:
194
AN:
79236
European-Finnish (FIN)
AF:
AC:
916
AN:
48324
Middle Eastern (MID)
AF:
AC:
1
AN:
5700
European-Non Finnish (NFE)
AF:
AC:
9437
AN:
1079056
Other (OTH)
AF:
AC:
347
AN:
58098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
0
756
1512
2269
3025
3781
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.00571 AC: 870AN: 152334Hom.: 9 Cov.: 33 AF XY: 0.00626 AC XY: 466AN XY: 74490 show subpopulations
GnomAD4 genome
AF:
AC:
870
AN:
152334
Hom.:
Cov.:
33
AF XY:
AC XY:
466
AN XY:
74490
show subpopulations
African (AFR)
AF:
AC:
64
AN:
41574
American (AMR)
AF:
AC:
23
AN:
15308
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5184
South Asian (SAS)
AF:
AC:
9
AN:
4826
European-Finnish (FIN)
AF:
AC:
219
AN:
10620
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
547
AN:
68028
Other (OTH)
AF:
AC:
8
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.487
Heterozygous variant carriers
0
41
83
124
166
207
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
CEP295NL: BS2 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
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
Publications
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