rs4680580

Positions:

• chr3-160397216-C-T

Variant summary

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

The NM_020800.3(IFT80):​c.-47+1930G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,868 control chromosomes in the GnomAD database, including 21,351 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 0.52 (21351 hom., cov: 32)
• Consequence: IFT80 NM_020800.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

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]

TRIM59-IFT80 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFT80	NM_020800.3	c.-47+1930G>A		intron_variant		ENST00000326448.12
TRIM59-IFT80	NR_148401.1	n.1148-31064G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFT80	ENST00000326448.12	c.-47+1930G>A		intron_variant		1	NM_020800.3	P1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79571 AN: 151750 Hom.: 21313 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.525 AC: 79674 AN: 151868 Hom.: 21351 Cov.: 32 AF XY: 0.522 AC XY: 38735 AN XY: 74236

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.486

Alfa AF: 0.527 Hom.: 7933

Bravo AF: 0.516

Asia WGS AF: 0.384 AC: 1336 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.17

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: rs4680580; hg19: chr3-160115004;