chr3-160356979-A-G

Position:

• chr3-160356979-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020800.3(IFT80):​c.639+510T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,114 control chromosomes in the GnomAD database, including 12,727 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (12727 hom., cov: 32)
• Consequence: IFT80 NM_020800.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

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]

IFT80 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFT80	NM_020800.3	c.639+510T>C		intron_variant		ENST00000326448.12	NP_065851.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFT80	ENST00000326448.12	c.639+510T>C		intron_variant		1	NM_020800.3	ENSP00000312778.7
ENSG00000248710	ENST00000483754.1	n.1152+510T>C		intron_variant		2		ENSP00000456272.1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59483 AN: 151996 Hom.: 12714 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.377

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.391 AC: 59534 AN: 152114 Hom.: 12727 Cov.: 32 AF XY: 0.388 AC XY: 28841 AN XY: 74344

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.384

Alfa AF: 0.462 Hom.: 7855

Bravo AF: 0.377

Asia WGS AF: 0.287 AC: 998 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.71

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

Other links and lift over

dbSNP: rs6798183; hg19: chr3-160074767;