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

Variant summary

Our verdict is Benign. The variant received -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

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]

IFT80 links:

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]

TRIM59-IFT80 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 Benign/Likely_benign. ClinVar VariationId is 215528.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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

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
TRIM59-IFT80	ENST00000483754.1 link	n.2737-10delT		intron_variant	Intron 17 of 18	2		ENSP00000456272.1

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

GnomAD2 exomes

AF:

0.0282

AC:

5278

AN:

187270

AF XY:

0.0264

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 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

African (AFR)

AF:

0.0732

AC:

2268

AN:

30998

American (AMR)

AF:

0.0208

AC:

821

AN:

39550

Ashkenazi Jewish (ASJ)

AF:

0.0139

AC:

335

AN:

24154

East Asian (EAS)

AF:

0.000165

AC:

AN:

36298

South Asian (SAS)

AF:

0.00916

AC:

730

AN:

79692

European-Finnish (FIN)

AF:

0.0116

AC:

516

AN:

44498

Middle Eastern (MID)

AF:

0.0264

AC:

140

AN:

5296

European-Non Finnish (NFE)

AF:

0.0247

AC:

25869

AN:

1046030

Other (OTH)

AF:

0.0264

AC:

1483

AN:

56126

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1767

3535

5302

7070

8837

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

974

1948

2922

3896

4870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0335

AC:

4959

AN:

148044

Hom.:

115

Cov.:

AF XY:

0.0327

AC XY:

2354

AN XY:

72038

show subpopulations

African (AFR)

AF:

0.0657

AC:

2656

AN:

40414

American (AMR)

AF:

0.0276

AC:

407

AN:

14754

Ashkenazi Jewish (ASJ)

AF:

0.0117

AC:

AN:

3430

East Asian (EAS)

AF:

0.00

AC:

AN:

5036

South Asian (SAS)

AF:

0.00731

AC:

AN:

4654

European-Finnish (FIN)

AF:

0.0114

AC:

111

AN:

9718

Middle Eastern (MID)

AF:

0.0524

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.0243

AC:

1622

AN:

66812

Other (OTH)

AF:

0.0362

AC:

AN:

2046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

246

493

739

986

1232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<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:

0.0149

Hom.:

500

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

PhyloP100

0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

3-160258644-GAAAA-GAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over