chr3-160310226-T-C

Position:

• chr3-160310226-T-C

Variant summary

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

The NM_020800.3(IFT80):​c.958-2445A>G 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 151,972 control chromosomes in the GnomAD database, including 21,398 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 0.53 (21398 hom., cov: 32)
• Consequence: IFT80 NM_020800.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFT80	NM_020800.3	c.958-2445A>G		intron_variant		ENST00000326448.12	NP_065851.1
TRIM59-IFT80	NR_148401.1	n.1666-2445A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFT80	ENST00000326448.12	c.958-2445A>G		intron_variant		1	NM_020800.3	ENSP00000312778	P1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79696 AN: 151854 Hom.: 21360 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.525 AC: 79798 AN: 151972 Hom.: 21398 Cov.: 32 AF XY: 0.522 AC XY: 38789 AN XY: 74290

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.488

Alfa AF: 0.533 Hom.: 11569

Bravo AF: 0.516

Asia WGS AF: 0.384 AC: 1338 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.1
DANN	Benign	0.67

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: rs4679881; hg19: chr3-160028014;