rs140627086
Positions:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004715.5(CTDP1):c.2274G>A(p.Pro758=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00509 in 1,613,568 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0029 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0053 ( 26 hom. )
Consequence
CTDP1
NM_004715.5 synonymous
NM_004715.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.57
Genes affected
CTDP1 (HGNC:2498): (CTD phosphatase subunit 1) This gene encodes a protein which interacts with the carboxy-terminus of the RAP74 subunit of transcription initiation factor TFIIF, and functions as a phosphatase that processively dephosphorylates the C-terminus of POLR2A (a subunit of RNA polymerase II), making it available for initiation of gene expression. Mutations in this gene are associated with congenital cataracts, facial dysmorphism and neuropathy syndrome (CCFDN). Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 18-79717873-G-A is Benign according to our data. Variant chr18-79717873-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 210803.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-79717873-G-A is described in Lovd as [Likely_benign]. Variant chr18-79717873-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-1.58 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome4 at 26 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTDP1 | NM_004715.5 | c.2274G>A | p.Pro758= | synonymous_variant | 10/13 | ENST00000613122.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTDP1 | ENST00000613122.5 | c.2274G>A | p.Pro758= | synonymous_variant | 10/13 | 1 | NM_004715.5 | P1 | |
CTDP1 | ENST00000075430.11 | c.2274G>A | p.Pro758= | synonymous_variant | 10/12 | 1 | |||
CTDP1 | ENST00000591598.5 | c.2070G>A | p.Pro690= | synonymous_variant | 10/12 | 1 | |||
CTDP1 | ENST00000299543.9 | c.897G>A | p.Pro299= | synonymous_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00288 AC: 438AN: 152184Hom.: 1 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
438
AN:
152184
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:
GnomAD3 exomes AF: 0.00325 AC: 815AN: 250840Hom.: 2 AF XY: 0.00328 AC XY: 445AN XY: 135736
GnomAD3 exomes
AF:
AC:
815
AN:
250840
Hom.:
AF XY:
AC XY:
445
AN XY:
135736
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00531 AC: 7765AN: 1461266Hom.: 26 Cov.: 35 AF XY: 0.00519 AC XY: 3772AN XY: 726976
GnomAD4 exome
AF:
AC:
7765
AN:
1461266
Hom.:
Cov.:
35
AF XY:
AC XY:
3772
AN XY:
726976
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00289 AC: 440AN: 152302Hom.: 1 Cov.: 33 AF XY: 0.00263 AC XY: 196AN XY: 74474
GnomAD4 genome
?
AF:
AC:
440
AN:
152302
Hom.:
Cov.:
33
AF XY:
AC XY:
196
AN XY:
74474
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
8
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 17, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 12, 2016 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | CTDP1: BP4, BP7 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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