NM_020800.3:c.639+510T>C

Variant names:

• chr3-160356979-A-G
• rs6798183
• NM_020800.3:c.639+510T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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: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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020800.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFT80	NM_020800.3	MANE Select	c.639+510T>C		intron	N/A	NP_065851.1
	IFT80	NM_001190241.2		c.228+510T>C		intron	N/A	NP_001177170.1
	IFT80	NM_001190242.2		c.228+510T>C		intron	N/A	NP_001177171.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFT80	ENST00000326448.12	TSL:1 MANE Select	c.639+510T>C		intron	N/A	ENSP00000312778.7
	IFT80	ENST00000483465.5	TSL:1	c.228+510T>C		intron	N/A	ENSP00000418196.1
	TRIM59-IFT80	ENST00000483754.1	TSL:2	n.1152+510T>C		intron	N/A	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

African (AFR) AF: 0.245 AC: 10173 AN: 41504

American (AMR) AF: 0.377 AC: 5765 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3468

East Asian (EAS) AF: 0.184 AC: 953 AN: 5174

South Asian (SAS) AF: 0.350 AC: 1687 AN: 4824

European-Finnish (FIN) AF: 0.477 AC: 5041 AN: 10560

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33038 AN: 67980

Other (OTH) AF: 0.384 AC: 810 AN: 2112

Alfa AF: 0.461 Hom.: 8764

Bravo AF: 0.377

Asia WGS AF: 0.287 AC: 998 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.71
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6798183; hg19: chr3-160074767;