GeneBe

rs1212853305

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000492.4(CFTR):​c.54-2497_54-2482delAAAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., cov: 0)

Consequence

CFTR
NM_000492.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.779

Publications

0 publications found
Variant links:
Genes affected
CFTR (HGNC:1884): (CF transmembrane conductance regulator) This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. The encoded protein functions as a chloride channel, making it unique among members of this protein family, and controls ion and water secretion and absorption in epithelial tissues. Channel activation is mediated by cycles of regulatory domain phosphorylation, ATP-binding by the nucleotide-binding domains, and ATP hydrolysis. Mutations in this gene cause cystic fibrosis, the most common lethal genetic disorder in populations of Northern European descent. The most frequently occurring mutation in cystic fibrosis, DeltaF508, results in impaired folding and trafficking of the encoded protein. Multiple pseudogenes have been identified in the human genome. [provided by RefSeq, Aug 2017]
CFTR Gene-Disease associations (from GenCC):
  • cystic fibrosis
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Myriad Women’s Health, Laboratory for Molecular Medicine
  • congenital bilateral absence of vas deferens
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • hereditary chronic pancreatitis
    Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000492.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CFTR
NM_000492.4
MANE Select
c.54-2497_54-2482delAAAAAAAAAAAAAAAA
intron
N/ANP_000483.3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CFTR
ENST00000003084.11
TSL:1 MANE Select
c.54-2505_54-2490delAAAAAAAAAAAAAAAA
intron
N/AENSP00000003084.6P13569-1
CFTR
ENST00000546407.1
TSL:1
n.167-2505_167-2490delAAAAAAAAAAAAAAAA
intron
N/A
CFTR
ENST00000699602.1
c.54-2505_54-2490delAAAAAAAAAAAAAAAA
intron
N/AENSP00000514471.1A0A8V8TNH2

Frequencies

GnomAD3 genomes
AF:
0.000137
AC:
6
AN:
43902
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000403
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.000137
AC:
6
AN:
43902
Hom.:
0
Cov.:
0
AF XY:
0.000102
AC XY:
2
AN XY:
19670
show subpopulations
African (AFR)
AF:
0.000403
AC:
6
AN:
14870
American (AMR)
AF:
0.00
AC:
0
AN:
3220
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
950
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1556
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1048
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
508
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
30
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
21034
Other (OTH)
AF:
0.00
AC:
0
AN:
494
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.633
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1212853305; hg19: chr7-117141801; API