NM_001371623.1(TCOF1):c.1120G>T (p.Ala374Ser) AND not provided

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Feb 27, 2019
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000425058.9

Allele description [Variation Report for NM_001371623.1(TCOF1):c.1120G>T (p.Ala374Ser)]

NM_001371623.1(TCOF1):c.1120G>T (p.Ala374Ser)

Gene:

TCOF1:treacle ribosome biogenesis factor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q32

Genomic location:

Preferred name:

NM_001371623.1(TCOF1):c.1120G>T (p.Ala374Ser)

HGVS:

NC_000005.10:g.150374653G>T
NG_011341.1:g.22015G>T
NM_000356.4:c.889G>T
NM_001008657.3:c.1120G>T
NM_001135243.2:c.1120G>T
NM_001135244.2:c.1120G>T
NM_001135245.2:c.889G>T
NM_001195141.2:c.1120G>T
NM_001371623.1:c.1120G>TMANE SELECT
NP_000347.2:p.Ala297Ser
NP_001008657.1:p.Ala374Ser
NP_001128715.1:p.Ala374Ser
NP_001128715.1:p.Ala374Ser
NP_001128716.1:p.Ala374Ser
NP_001128717.1:p.Ala297Ser
NP_001182070.1:p.Ala374Ser
NP_001358552.1:p.Ala374Ser
NC_000005.9:g.149754216G>T
NM_001135243.1:c.1120G>T

Protein change:

A297S

Links:

dbSNP: rs112039991

NCBI 1000 Genomes Browser:

rs112039991

Molecular consequence:

NM_000356.4:c.889G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001008657.3:c.1120G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001135243.2:c.1120G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001135244.2:c.1120G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001135245.2:c.889G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195141.2:c.1120G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001371623.1:c.1120G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000511274	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Jan 11, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001146127	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Feb 26, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001891673	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Feb 27, 2019)	germline	clinical testing	Citation Link,
SCV005221344	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000511274.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Converted during submission to Likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.000811	not provided	not provided

From Athena Diagnostics, SCV001146127.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001891673.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005221344.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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