Variant rs8084175 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.383

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:

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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	Protein	UniProt
CTDP1	NM_004715.5 linkuse as main transcript	c.2069-20C>T		intron_variant		ENST00000613122.5	NP_004706.3	Q9Y5B0-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CTDP1	ENST00000613122.5 linkuse as main transcript	c.2069-20C>T	intron_variant	1	NM_004715.5	ENSP00000484525.2	Q9Y5B0-1
CTDP1	ENST00000075430.11 linkuse as main transcript	c.2069-20C>T	intron_variant	1		ENSP00000075430.7	Q9Y5B0-4
CTDP1	ENST00000591598.5 linkuse as main transcript	c.1865-20C>T	intron_variant	1		ENSP00000465119.1	K7EJD2
CTDP1	ENST00000299543.9 linkuse as main transcript	c.689-20C>T	intron_variant	5		ENSP00000299543.9	A0A0A0MR03

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19166

AN:

152092

Hom.:

1598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0332

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.0938

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.0682

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.110

GnomAD3 exomes

AF:

0.136

AC:

33620

AN:

248056

Hom.:

2769

AF XY:

0.136

AC XY:

18293

AN XY:

134494

show subpopulations

Gnomad AFR exome

AF:

0.0313

Gnomad AMR exome

AF:

0.0789

Gnomad ASJ exome

AF:

0.106

Gnomad EAS exome

AF:

0.123

Gnomad SAS exome

AF:

0.0730

Gnomad FIN exome

AF:

0.181

Gnomad NFE exome

AF:

0.181

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.172

AC:

251683

AN:

1459122

Hom.:

23561

Cov.:

AF XY:

0.169

AC XY:

122971

AN XY:

725900

show subpopulations

Gnomad4 AFR exome

AF:

0.0274

Gnomad4 AMR exome

AF:

0.0810

Gnomad4 ASJ exome

AF:

0.103

Gnomad4 EAS exome

AF:

0.0932

Gnomad4 SAS exome

AF:

0.0743

Gnomad4 FIN exome

AF:

0.185

Gnomad4 NFE exome

AF:

0.193

Gnomad4 OTH exome

AF:

0.161

GnomAD4 genome

AF:

0.126

AC:

19159

AN:

152210

Hom.:

1597

Cov.:

AF XY:

0.123

AC XY:

9121

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0331

Gnomad4 AMR

AF:

0.0937

Gnomad4 ASJ

AF:

0.101

Gnomad4 EAS

AF:

0.119

Gnomad4 SAS

AF:

0.0683

Gnomad4 FIN

AF:

0.177

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.108

Alfa

AF:

0.151

Hom.:

363

Bravo

AF:

0.116

Asia WGS

AF:

0.0860

AC:

301

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.3

DANN

Benign

0.56

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.

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