GeneBe

rs57319132

Variant names:

Variant summary

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

The NM_000492.4(CFTR):​c.3964-2695_3964-2682delAAAAAAAAAAAAAA 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 0.000057 ( 0 hom., cov: 0)

Consequence

CFTR
NM_000492.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.05
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CFTRNM_000492.4 linkc.3964-2695_3964-2682delAAAAAAAAAAAAAA intron_variant Intron 24 of 26 ENST00000003084.11 NP_000483.3 P13569-1A0A024R730

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CFTRENST00000003084.11 linkc.3964-2704_3964-2691delAAAAAAAAAAAAAA intron_variant Intron 24 of 26 1 NM_000492.4 ENSP00000003084.6 P13569-1

Frequencies

GnomAD3 genomes
AF:
0.0000571
AC:
5
AN:
87494
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000190
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:
0.0000571
AC:
5
AN:
87540
Hom.:
0
Cov.:
0
AF XY:
0.0000247
AC XY:
1
AN XY:
40486
show subpopulations
African (AFR)
AF:
0.000189
AC:
5
AN:
26424
American (AMR)
AF:
0.00
AC:
0
AN:
7620
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2076
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2594
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2334
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2340
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
140
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
42246
Other (OTH)
AF:
0.00
AC:
0
AN:
1180
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.645
Heterozygous variant carriers
0
1
1
2
2
3
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 v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.1

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 for variant 7:117661983 GAAAAAAAAAAAAAA>G . It may be empty.

Other links and lift over

dbSNP: rs57319132; hg19: chr7-117302037; API