NM_000492.4(CFTR):c.1657C>T (p.Arg553Ter) AND Bronchiectasis with or without elevated sweat chloride 1

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 26, 2024
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:: RCV003137499.10

Allele description [Variation Report for NM_000492.4(CFTR):c.1657C>T (p.Arg553Ter)]

NM_000492.4(CFTR):c.1657C>T (p.Arg553Ter)

Genes:

CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]
LOC111674475:CFTR intron 11 enhancer [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

7q31.2

Genomic location:

Preferred name:

NM_000492.4(CFTR):c.1657C>T (p.Arg553Ter)

HGVS:

NC_000007.14:g.117587811C>T
NG_016465.4:g.127028C>T
NG_056131.3:g.766C>T
NM_000492.4:c.1657C>TMANE SELECT
NP_000483.3:p.Arg553Ter
NP_000483.3:p.Arg553Ter
LRG_663t1:c.1657C>T
LRG_663:g.127028C>T
LRG_663p1:p.Arg553Ter
NC_000007.13:g.117227865C>T
NM_000492.3:c.1657C>T
p.Arg553*
p.Arg553X

Protein change:

R553*; ARG553TER

Links:

Genetic Testing Registry (GTR): GTR000500233; OMIM: 602421.0014; dbSNP: rs74597325

NCBI 1000 Genomes Browser:

rs74597325

Molecular consequence:

NM_000492.4:c.1657C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Bronchiectasis with or without elevated sweat chloride 1 (BESC1)
Synonyms:: Cystic Fibrosis-Like Syndrome
Identifiers:: MONDO: MONDO:0008887; MedGen: C2749757; Orphanet: 60033; OMIM: 211400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003806966	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 29, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004213271	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 26, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003806966

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 29, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004213271

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 26, 2024)

unknown

clinical testing

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

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 Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV003806966.1

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

Description

ACMG classification criteria: PVS1 very strong, PM2 supporting, PM3 strong, PP1 supporting

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

From Baylor Genetics, SCV004213271.2

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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