rs528897827

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBS1BS2

The NM_001371623.1(TCOF1):c.827_844delGATCTGAAAGTGAGGAGG(p.Gly276_Glu281del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00362 in 1,612,938 control chromosomes in the GnomAD database, including 23 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0026 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0037 ( 22 hom. )

Consequence

TCOF1
NM_001371623.1 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 3.76

Variant links:

Genes affected

TCOF1 (HGNC:11654): (treacle ribosome biogenesis factor 1) This gene encodes a nucleolar protein with a LIS1 homology domain. The protein is involved in ribosomal DNA gene transcription through its interaction with upstream binding factor (UBF). Mutations in this gene have been associated with Treacher Collins syndrome, a disorder which includes abnormal craniofacial development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

TCOF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001371623.1.

BP6

Variant 5-150372182-TAGTGAGGAGGGATCTGAA-T is Benign according to our data. Variant chr5-150372182-TAGTGAGGAGGGATCTGAA-T is described in ClinVar as [Likely_benign]. Clinvar id is 431981.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-150372182-TAGTGAGGAGGGATCTGAA-T is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00257 (388/151240) while in subpopulation AMR AF= 0.00486 (74/15214). AF 95% confidence interval is 0.00397. There are 1 homozygotes in gnomad4. There are 191 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 388 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCOF1	NM_001371623.1 link	c.827_844delGATCTGAAAGTGAGGAGG	p.Gly276_Glu281del	disruptive_inframe_deletion	Exon 7 of 27	ENST00000643257.2	NP_001358552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCOF1	ENST00000643257.2 link	c.827_844delGATCTGAAAGTGAGGAGG	p.Gly276_Glu281del	disruptive_inframe_deletion	Exon 7 of 27		NM_001371623.1	ENSP00000493815.1		Q13428-3

Frequencies

GnomAD3 genomes

AF:

0.00257

AC:

388

AN:

151122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000755

Gnomad AMI

AF:

0.00222

Gnomad AMR

AF:

0.00487

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000840

Gnomad FIN

AF:

0.00315

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00353

Gnomad OTH

AF:

0.00242

GnomAD3 exomes

AF:

0.00196

AC:

488

AN:

248872

Hom.:

AF XY:

0.00203

AC XY:

274

AN XY:

135082

show subpopulations

Gnomad AFR exome

AF:

0.000260

Gnomad AMR exome

AF:

0.00136

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00154

Gnomad FIN exome

AF:

0.00140

Gnomad NFE exome

AF:

0.00306

Gnomad OTH exome

AF:

0.00248

GnomAD4 exome

AF:

0.00373

AC:

5458

AN:

1461698

Hom.:

AF XY:

0.00358

AC XY:

2605

AN XY:

727146

show subpopulations

Gnomad4 AFR exome

AF:

0.000657

Gnomad4 AMR exome

AF:

0.00148

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00154

Gnomad4 FIN exome

AF:

0.00155

Gnomad4 NFE exome

AF:

0.00446

Gnomad4 OTH exome

AF:

0.00313

GnomAD4 genome

AF:

0.00257

AC:

388

AN:

151240

Hom.:

Cov.:

AF XY:

0.00259

AC XY:

191

AN XY:

73854

show subpopulations

Gnomad4 AFR

AF:

0.000753

Gnomad4 AMR

AF:

0.00486

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000841

Gnomad4 FIN

AF:

0.00315

Gnomad4 NFE

AF:

0.00353

Gnomad4 OTH

AF:

0.00239

Alfa

AF:

0.00229

Hom.:

Bravo

AF:

0.00271

EpiCase

AF:

0.00316

EpiControl

AF:

0.00350

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

May 01, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 22317976) -

Jun 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

TCOF1: BS2 -

May 12, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 02, 2019

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Feb 06, 2017

Eurofins Ntd Llc (ga)

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Treacher Collins syndrome 1

Benign:1

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

TCOF1-related disorder

Benign:1

Jun 08, 2020

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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