rs3027234

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_025099.6(CTC1):​c.1945+132G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 1,220,852 control chromosomes in the GnomAD database, including 25,361 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2220 hom., cov: 32)
Exomes 𝑓: 0.20 ( 23141 hom. )

Consequence

CTC1
NM_025099.6 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.282
Variant links:
Genes affected
CTC1 (HGNC:26169): (CST telomere replication complex component 1) This gene encodes a component of the CST complex. This complex plays an essential role in protecting telomeres from degradation. This protein also forms a heterodimer with the CST complex subunit STN1 to form the enzyme alpha accessory factor. This enzyme regulates DNA replication. Mutations in this gene are the cause of cerebroretinal microangiopathy with calcifications and cysts. Alternate splicing results in both coding and non-coding variants. [provided by RefSeq, Mar 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 17-8232774-C-T is Benign according to our data. Variant chr17-8232774-C-T is described in ClinVar as [Benign]. Clinvar id is 1233975.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-8232774-C-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTC1NM_025099.6 linkuse as main transcriptc.1945+132G>A intron_variant ENST00000651323.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTC1ENST00000651323.1 linkuse as main transcriptc.1945+132G>A intron_variant NM_025099.6 P1Q2NKJ3-1

Frequencies

GnomAD3 genomes
AF:
0.156
AC:
23739
AN:
152082
Hom.:
2219
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0664
Gnomad AMI
AF:
0.211
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.223
Gnomad EAS
AF:
0.0434
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.152
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.223
Gnomad OTH
AF:
0.149
GnomAD4 exome
AF:
0.201
AC:
214365
AN:
1068650
Hom.:
23141
Cov.:
14
AF XY:
0.199
AC XY:
107083
AN XY:
537036
show subpopulations
Gnomad4 AFR exome
AF:
0.0606
Gnomad4 AMR exome
AF:
0.105
Gnomad4 ASJ exome
AF:
0.219
Gnomad4 EAS exome
AF:
0.0333
Gnomad4 SAS exome
AF:
0.122
Gnomad4 FIN exome
AF:
0.158
Gnomad4 NFE exome
AF:
0.226
Gnomad4 OTH exome
AF:
0.187
GnomAD4 genome
AF:
0.156
AC:
23745
AN:
152202
Hom.:
2220
Cov.:
32
AF XY:
0.151
AC XY:
11230
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.0664
Gnomad4 AMR
AF:
0.138
Gnomad4 ASJ
AF:
0.223
Gnomad4 EAS
AF:
0.0433
Gnomad4 SAS
AF:
0.110
Gnomad4 FIN
AF:
0.152
Gnomad4 NFE
AF:
0.223
Gnomad4 OTH
AF:
0.148
Alfa
AF:
0.171
Hom.:
499
Bravo
AF:
0.152
Asia WGS
AF:
0.0710
AC:
245
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 27, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.1
DANN
Benign
0.62
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3027234; hg19: chr17-8136092; API