rs6441306

Positions:

• chr3-160234491-A-G

Variant summary

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

The ENST00000483754.1(ENSG00000248710):​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: ENSG00000248710 ENST00000483754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

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]

TRIM59-IFT80 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TRIM59-IFT80	NR_148401.1	n.3101-6769T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000248710	ENST00000483754.1	n.*59-6769T>C		intron_variant		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

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.434

Alfa AF: 0.449 Hom.: 11711

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

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: rs6441306; hg19: chr3-159952278;