rs8084175
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004715.5(CTDP1):c.2069-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 1,611,332 control chromosomes in the GnomAD database, including 25,158 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.13 ( 1597 hom., cov: 34)
Exomes 𝑓: 0.17 ( 23561 hom. )
Consequence
CTDP1
NM_004715.5 intron
NM_004715.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.383
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 18-79717515-C-T is Benign according to our data. Variant chr18-79717515-C-T is described in ClinVar as [Benign]. Clinvar id is 259523.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-79717515-C-T is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTDP1 | NM_004715.5 | c.2069-20C>T | intron_variant | ENST00000613122.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTDP1 | ENST00000613122.5 | c.2069-20C>T | intron_variant | 1 | NM_004715.5 | P1 | |||
CTDP1 | ENST00000075430.11 | c.2069-20C>T | intron_variant | 1 | |||||
CTDP1 | ENST00000591598.5 | c.1865-20C>T | intron_variant | 1 | |||||
CTDP1 | ENST00000299543.9 | c.691-20C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.126 AC: 19166AN: 152092Hom.: 1598 Cov.: 34
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GnomAD3 exomes AF: 0.136 AC: 33620AN: 248056Hom.: 2769 AF XY: 0.136 AC XY: 18293AN XY: 134494
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GnomAD4 exome AF: 0.172 AC: 251683AN: 1459122Hom.: 23561 Cov.: 38 AF XY: 0.169 AC XY: 122971AN XY: 725900
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GnomAD4 genome ? AF: 0.126 AC: 19159AN: 152210Hom.: 1597 Cov.: 34 AF XY: 0.123 AC XY: 9121AN XY: 74424
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at