rs58665245

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The ENST00000326448.12(IFT80):​c.2224-13_2224-10del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000594 in 1,514,150 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000044 ( 0 hom. )

Consequence

IFT80
ENST00000326448.12 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.62
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 3-160258644-GAAAA-G is Benign according to our data. Variant chr3-160258644-GAAAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 1590050.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IFT80NM_020800.3 linkuse as main transcriptc.2224-13_2224-10del splice_polypyrimidine_tract_variant, intron_variant ENST00000326448.12 NP_065851.1
TRIM59-IFT80NR_148401.1 linkuse as main transcriptn.2932-13_2932-10del splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IFT80ENST00000326448.12 linkuse as main transcriptc.2224-13_2224-10del splice_polypyrimidine_tract_variant, intron_variant 1 NM_020800.3 ENSP00000312778 P1Q9P2H3-1

Frequencies

GnomAD3 genomes
AF:
0.0000203
AC:
3
AN:
147972
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000744
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
GnomAD3 exomes
AF:
0.00000534
AC:
1
AN:
187270
Hom.:
0
AF XY:
0.00000986
AC XY:
1
AN XY:
101404
show subpopulations
Gnomad AFR exome
AF:
0.0000743
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000439
AC:
6
AN:
1366178
Hom.:
0
AF XY:
0.00000441
AC XY:
3
AN XY:
679782
show subpopulations
Gnomad4 AFR exome
AF:
0.000193
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000203
AC:
3
AN:
147972
Hom.:
0
Cov.:
0
AF XY:
0.0000278
AC XY:
2
AN XY:
71944
show subpopulations
Gnomad4 AFR
AF:
0.0000744
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Jeune thoracic dystrophy Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 17, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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. It may be empty.

Other links and lift over

dbSNP: rs58665245; hg19: chr3-159976432; API