NM_000492.4(CFTR):c.490-9T>A AND Cystic fibrosis

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 5, 2023
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:: RCV001419336.9

Allele description [Variation Report for NM_000492.4(CFTR):c.490-9T>A]

NM_000492.4(CFTR):c.490-9T>A

Gene:

CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q31.2

Genomic location:

Preferred name:

NM_000492.4(CFTR):c.490-9T>A

HGVS:

NC_000007.14:g.117534267T>A
NG_016465.4:g.73484T>A
NM_000492.3:c.490-9T>A
NM_000492.4:c.490-9T>AMANE SELECT
LRG_663t1:c.490-9T>A
LRG_663:g.73484T>A
NC_000007.13:g.117174321T>A
NM_000492.4:c.490-9T>A

Links:

dbSNP: rs2116674841

NCBI 1000 Genomes Browser:

rs2116674841

Molecular consequence:

NM_000492.4:c.490-9T>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Cystic fibrosis (CF)
Synonyms:: Mucoviscidosis
Identifiers:: MONDO: MONDO:0009061; MedGen: C0010674; Orphanet: 586; OMIM: 219700

Recent activity

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receptor tyrosine-protein kinase erbB-3 isoform 1 precursor [Homo sapiens]
receptor tyrosine-protein kinase erbB-3 isoform 1 precursor [Homo sapiens]
gi|54792100|ref|NP_001973.2|

Protein
Mugil liza isolate MPL22 tRNA-Thr gene, partial sequence; tRNA-Pro gene, complet...
Mugil liza isolate MPL22 tRNA-Thr gene, partial sequence; tRNA-Pro gene, complete sequence; and control region, partial sequence; mitochondrial
gi|937965279|gb|KP875727.1|

Nucleotide
Mugil liza isolate MPL26 tRNA-Thr gene, partial sequence; tRNA-Pro gene, complet...
Mugil liza isolate MPL26 tRNA-Thr gene, partial sequence; tRNA-Pro gene, complete sequence; and control region, partial sequence; mitochondrial
gi|937965282|gb|KP875730.1|

Nucleotide
cytochrome c oxidase subunit I, partial (mitochondrion) [Mugil liza]
cytochrome c oxidase subunit I, partial (mitochondrion) [Mugil liza]
gi|203284864|gb|ACH97070.1|

Protein
Mugil liza isolate MPL3 tRNA-Thr gene, partial sequence; tRNA-Pro gene, complete...
Mugil liza isolate MPL3 tRNA-Thr gene, partial sequence; tRNA-Pro gene, complete sequence; and control region, partial sequence; mitochondrial
gi|937965276|gb|KP875724.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001621588	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jun 24, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003870713	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jan 5, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001621588

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jun 24, 2020)

germline

clinical testing

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

SCV003870713

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jan 5, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001621588.4

#	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 Ambry Genetics, SCV003870713.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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

Last Updated: Oct 26, 2024

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