chr3-160319837-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_020800.3(IFT80):​c.880G>T​(p.Val294Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,460,988 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: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

IFT80
NM_020800.3 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.77
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]
ENSG00000248710 (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 made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IFT80NM_020800.3 linkc.880G>T p.Val294Phe missense_variant 9/20 ENST00000326448.12 NP_065851.1 Q9P2H3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IFT80ENST00000326448.12 linkc.880G>T p.Val294Phe missense_variant 9/201 NM_020800.3 ENSP00000312778.7 Q9P2H3-1
ENSG00000248710ENST00000483754.1 linkn.1393G>T non_coding_transcript_exon_variant 7/192 ENSP00000456272.1 H3BRJ5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
250988
Hom.:
0
AF XY:
0.00000737
AC XY:
1
AN XY:
135626
show subpopulations
Gnomad AFR exome
AF:
0.00
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:
0.00000881
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1460988
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
726790
show subpopulations
Gnomad4 AFR exome
AF:
0.00
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:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
-0.039
T
BayesDel_noAF
Benign
-0.29
CADD
Uncertain
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.18
T;.;.
Eigen
Benign
-0.12
Eigen_PC
Benign
0.055
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.95
D;.;D
M_CAP
Benign
0.0055
T
MetaRNN
Uncertain
0.54
D;D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.34
N;.;.
PrimateAI
Uncertain
0.58
T
PROVEAN
Benign
-2.1
N;D;D
REVEL
Benign
0.18
Sift
Benign
0.11
T;D;D
Sift4G
Benign
0.22
T;T;T
Polyphen
0.59
P;.;.
Vest4
0.72
MutPred
0.52
Loss of sheet (P = 0.1398);.;.;
MVP
0.29
MPC
0.21
ClinPred
0.61
D
GERP RS
4.7
Varity_R
0.16
gMVP
0.64

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: rs148926415; hg19: chr3-160037625; API