18-79710834-C-T

Variant names:

• chr18-79710834-C-T
• rs676713
• NM_004715.5:c.863+398C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004715.5(CTDP1):​c.863+398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 151,818 control chromosomes in the GnomAD database, including 44,236 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.76 (44236 hom., cov: 29)
• Consequence: CTDP1 NM_004715.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.543
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• congenital cataracts-facial dysmorphism-neuropathy syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 18-79710834-C-T is Benign according to our data. Variant chr18-79710834-C-T is described in ClinVar as Benign. ClinVar VariationId is 259524.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTDP1	NM_004715.5	c.863+398C>T		intron_variant	Intron 6 of 12	ENST00000613122.5	NP_004706.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTDP1	ENST00000613122.5	c.863+398C>T		intron_variant	Intron 6 of 12	1	NM_004715.5	ENSP00000484525.2
CTDP1	ENST00000075430.11	c.863+398C>T		intron_variant	Intron 6 of 11	1		ENSP00000075430.7
CTDP1	ENST00000591598.5	c.659+398C>T		intron_variant	Intron 6 of 11	1		ENSP00000465119.1

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115475 AN: 151700 Hom.: 44208 Cov.: 29

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.759

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.761 AC: 115550 AN: 151818 Hom.: 44236 Cov.: 29 AF XY: 0.765 AC XY: 56746 AN XY: 74186

African (AFR) AF: 0.703 AC: 29061 AN: 41310

American (AMR) AF: 0.742 AC: 11324 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2645 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3547 AN: 5134

South Asian (SAS) AF: 0.783 AC: 3760 AN: 4800

European-Finnish (FIN) AF: 0.872 AC: 9229 AN: 10580

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53375 AN: 67954

Other (OTH) AF: 0.756 AC: 1590 AN: 2104

Alfa AF: 0.772 Hom.: 5567

Bravo AF: 0.745

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.096
DANN	Benign	0.47
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs676713; hg19: chr18-77470834;