NM_004715.5:c.2817T>C

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_004715.5(CTDP1):c.2817T>C(p.Asp939Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.979 in 1,614,048 control chromosomes in the GnomAD database, including 777,656 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.91 ( 64273 hom., cov: 33)

Exomes 𝑓: 0.99 ( 713383 hom. )

Consequence

CTDP1
NM_004715.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.0560

Variant links:

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]

CTDP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 18-79753721-T-C is Benign according to our data. Variant chr18-79753721-T-C is described in ClinVar as [Benign]. Clinvar id is 128865.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-79753721-T-C is described in Lovd as [Benign]. Variant chr18-79753721-T-C is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=0.056 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTDP1	NM_004715.5 link	c.2817T>C	p.Asp939Asp	synonymous_variant	Exon 13 of 13	ENST00000613122.5	NP_004706.3	Q9Y5B0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTDP1	ENST00000613122.5 link	c.2817T>C	p.Asp939Asp	synonymous_variant	Exon 13 of 13	1	NM_004715.5	ENSP00000484525.2		Q9Y5B0-1

Frequencies

GnomAD3 genomes

AF:

0.910

AC:

138390

AN:

152116

Hom.:

64241

Cov.:

show subpopulations

Gnomad AFR

AF:

0.701

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.962

Gnomad ASJ

AF:

0.912

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.987

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.943

Gnomad NFE

AF:

0.997

Gnomad OTH

AF:

0.923

GnomAD3 exomes

AF:

0.971

AC:

243695

AN:

250934

Hom.:

119022

AF XY:

0.977

AC XY:

132613

AN XY:

135766

show subpopulations

Gnomad AFR exome

AF:

0.701

Gnomad AMR exome

AF:

0.980

Gnomad ASJ exome

AF:

0.921

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.988

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

0.997

Gnomad OTH exome

AF:

0.975

GnomAD4 exome

AF:

0.987

AC:

1442466

AN:

1461814

Hom.:

713383

Cov.:

AF XY:

0.988

AC XY:

718243

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.695

Gnomad4 AMR exome

AF:

0.977

Gnomad4 ASJ exome

AF:

0.918

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.989

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.997

Gnomad4 OTH exome

AF:

0.970

GnomAD4 genome

AF:

0.910

AC:

138475

AN:

152234

Hom.:

64273

Cov.:

AF XY:

0.913

AC XY:

67951

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.701

Gnomad4 AMR

AF:

0.963

Gnomad4 ASJ

AF:

0.912

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.987

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.997

Gnomad4 OTH

AF:

0.924

Alfa

AF:

0.952

Hom.:

36940

Bravo

AF:

0.897

Asia WGS

AF:

0.971

AC:

3376

AN:

3478

EpiCase

AF:

0.994

EpiControl

AF:

0.994

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Congenital cataracts-facial dysmorphism-neuropathy syndrome

Benign:2

Jul 30, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

5.0

DANN

Benign

0.59

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over