GeneBe

3-160258644-GAAAA-GAAAAAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_020800.3(IFT80):​c.2224-12_2224-10dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000732 in 1,366,092 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 7.3e-7 ( 0 hom. )

Consequence

IFT80
NM_020800.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.523

Publications

0 publications found
Variant links:
Genes affected
IFT80 (HGNC:29262): (intraflagellar transport 80) The protein encoded by this gene is part of the intraflagellar transport complex B and is necessary for the function of motile and sensory cilia. Defects in this gene are a cause of asphyxiating thoracic dystrophy 2 (ATD2). Three transcript variants encoding two different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]
TRIM59-IFT80 (HGNC:56756): (TRIM59-IFT80 readthrough (NMD candidate)) This locus represents naturally occurring readthrough transcription between the neighboring TRIM59 (tripartite motif containing 59) and IFT80 (intraflagellar transport 80) genes on chromosome 3. The readthrough transcript is unlikely to produce a protein product. [provided by RefSeq, Jun 2017]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IFT80NM_020800.3 linkc.2224-12_2224-10dupTTT intron_variant Intron 19 of 19 ENST00000326448.12 NP_065851.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IFT80ENST00000326448.12 linkc.2224-10_2224-9insTTT intron_variant Intron 19 of 19 1 NM_020800.3 ENSP00000312778.7
TRIM59-IFT80ENST00000483754.1 linkn.2737-10_2737-9insTTT intron_variant Intron 17 of 18 2 ENSP00000456272.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.32e-7
AC:
1
AN:
1366092
Hom.:
0
Cov.:
32
AF XY:
0.00000147
AC XY:
1
AN XY:
679744
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
31042
American (AMR)
AF:
0.00
AC:
0
AN:
39808
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24208
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36468
South Asian (SAS)
AF:
0.00
AC:
0
AN:
80020
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
44660
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5318
European-Non Finnish (NFE)
AF:
9.54e-7
AC:
1
AN:
1048310
Other (OTH)
AF:
0.00
AC:
0
AN:
56258
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.52
Mutation Taster
=100/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs58665245; hg19: chr3-159976432; API