rs6441306

Variant names:

• chr3-160234491-A-G
• rs6441306
• ENST00000483754.1:n.*59-6769T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000483754.1(TRIM59-IFT80):​n.*59-6769T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,872 control chromosomes in the GnomAD database, including 19,641 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 0.49 (19641 hom., cov: 31)
• Consequence: TRIM59-IFT80 ENST00000483754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 5 publications found

Genes affected

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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM59-IFT80	NR_148401.1	n.3101-6769T>C		intron_variant	Intron 18 of 18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM59-IFT80	ENST00000483754.1	n.*59-6769T>C		intron_variant	Intron 18 of 18	2		ENSP00000456272.1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74326 AN: 151754 Hom.: 19588 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.490 AC: 74444 AN: 151872 Hom.: 19641 Cov.: 31 AF XY: 0.487 AC XY: 36164 AN XY: 74250

African (AFR) AF: 0.669 AC: 27713 AN: 41400

American (AMR) AF: 0.346 AC: 5280 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1597 AN: 3472

East Asian (EAS) AF: 0.118 AC: 611 AN: 5170

South Asian (SAS) AF: 0.337 AC: 1617 AN: 4804

European-Finnish (FIN) AF: 0.560 AC: 5893 AN: 10526

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30104 AN: 67924

Other (OTH) AF: 0.434 AC: 914 AN: 2106

Alfa AF: 0.453 Hom.: 38434

Bravo AF: 0.483

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-1.5

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: rs6441306; hg19: chr3-159952278;