Genetic Variant IFT80:c.2224-10delT (chr3-160258644-GA-G) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_020800.3(IFT80):c.2224-10delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0246 in 1,510,686 control chromosomes in the GnomAD database, including 528 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.033 ( 115 hom., cov: 0)

Exomes 𝑓: 0.024 ( 413 hom. )

Consequence

IFT80
NM_020800.3 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.523

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]

IFT80 links:

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]

ENSG00000248710 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 3-160258644-GA-G is Benign according to our data. Variant chr3-160258644-GA-G is described in ClinVar as [Likely_benign]. Clinvar id is 215528.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-160258644-GA-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFT80	NM_020800.3 link	c.2224-10delT		intron_variant	Intron 19 of 19	ENST00000326448.12	NP_065851.1	Q9P2H3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFT80	ENST00000326448.12 link	c.2224-10delT		intron_variant	Intron 19 of 19	1	NM_020800.3	ENSP00000312778.7		Q9P2H3-1
ENSG00000248710	ENST00000483754.1 link	n.2737-10delT		intron_variant	Intron 17 of 18	2		ENSP00000456272.1		H3BRJ5

Frequencies

GnomAD3 genomes

AF:

0.0334

AC:

4948

AN:

147952

Hom.:

115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0656

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0276

Gnomad ASJ

AF:

0.0117

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00772

Gnomad FIN

AF:

0.0114

Gnomad MID

AF:

0.0452

Gnomad NFE

AF:

0.0243

Gnomad OTH

AF:

0.0366

GnomAD3 exomes

AF:

0.0282

AC:

5278

AN:

187270

Hom.:

AF XY:

0.0264

AC XY:

2673

AN XY:

101404

show subpopulations

Gnomad AFR exome

AF:

0.0798

Gnomad AMR exome

AF:

0.0268

Gnomad ASJ exome

AF:

0.0168

Gnomad EAS exome

AF:

0.00122

Gnomad SAS exome

AF:

0.0121

Gnomad FIN exome

AF:

0.0151

Gnomad NFE exome

AF:

0.0320

Gnomad OTH exome

AF:

0.0280

GnomAD4 exome

AF:

0.0236

AC:

32168

AN:

1362642

Hom.:

413

Cov.:

AF XY:

0.0229

AC XY:

15541

AN XY:

677994

show subpopulations

Gnomad4 AFR exome

AF:

0.0732

Gnomad4 AMR exome

AF:

0.0208

Gnomad4 ASJ exome

AF:

0.0139

Gnomad4 EAS exome

AF:

0.000165

Gnomad4 SAS exome

AF:

0.00916

Gnomad4 FIN exome

AF:

0.0116

Gnomad4 NFE exome

AF:

0.0247

Gnomad4 OTH exome

AF:

0.0264

GnomAD4 genome

AF:

0.0335

AC:

4959

AN:

148044

Hom.:

115

Cov.:

AF XY:

0.0327

AC XY:

2354

AN XY:

72038

show subpopulations

Gnomad4 AFR

AF:

0.0657

Gnomad4 AMR

AF:

0.0276

Gnomad4 ASJ

AF:

0.0117

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00731

Gnomad4 FIN

AF:

0.0114

Gnomad4 NFE

AF:

0.0243

Gnomad4 OTH

AF:

0.0362

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Jeune thoracic dystrophy

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

May 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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.

3-160258644-GAAAA-GAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over