rs6441306

chr3-160234491-A-G

Variant summary

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

The NR_148401.1(TRIM59-IFT80):n.3101-6769T>C variant causes a intron, non coding transcript 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 NR_148401.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

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	UniProt
TRIM59-IFT80	NR_148401.1	n.3101-6769T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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;