17-15304047-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_031898.3(TEKT3):c.1362A>C(p.Thr454=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 1,613,930 control chromosomes in the GnomAD database, including 483,891 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 0.79 (47181 hom., cov: 31)
  • Exomes 𝑓: 0.77 (436710 hom.)
• Consequence: TEKT3 NM_031898.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

TEKT3 (HGNC:14293): (tektin 3) This gene product belongs to the tektin family of proteins. Tektins comprise a family of filament-forming proteins that are coassembled with tubulins to form ciliary and flagellar microtubules. The exact function of this gene is not known. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BP7: Synonymous conserved (PhyloP=-0.291 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT3	NM_031898.3	c.1362A>C	p.Thr454=	synonymous_variant	9/9	ENST00000395930.6
LOC124903932	XR_007065633.1	n.298-812T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT3	ENST00000395930.6	c.1362A>C	p.Thr454=	synonymous_variant	9/9	1	NM_031898.3	P1
	ENST00000654786.1	n.138-3614T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119578 AN: 151938 Hom.: 47158 Cov.: 31

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.772

GnomAD3 exomes AF: 0.773 AC: 194334 AN: 251436 Hom.: 75307 AF XY: 0.773 AC XY: 105105 AN XY: 135890

Gnomad AFR exome AF: 0.837

Gnomad AMR exome AF: 0.779

Gnomad ASJ exome AF: 0.748

Gnomad EAS exome AF: 0.691

Gnomad SAS exome AF: 0.805

Gnomad FIN exome AF: 0.797

Gnomad NFE exome AF: 0.765

Gnomad OTH exome AF: 0.759

GnomAD4 exome AF: 0.773 AC: 1129322 AN: 1461874 Hom.: 436710 Cov.: 69 AF XY: 0.773 AC XY: 562065 AN XY: 727238

Gnomad4 AFR exome AF: 0.834

Gnomad4 AMR exome AF: 0.775

Gnomad4 ASJ exome AF: 0.749

Gnomad4 EAS exome AF: 0.685

Gnomad4 SAS exome AF: 0.805

Gnomad4 FIN exome AF: 0.796

Gnomad4 NFE exome AF: 0.771

Gnomad4 OTH exome AF: 0.769

GnomAD4 genome AF: 0.787 AC: 119643 AN: 152056 Hom.: 47181 Cov.: 31 AF XY: 0.786 AC XY: 58412 AN XY: 74320

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.772

Alfa AF: 0.763 Hom.: 42093

Bravo AF: 0.784

Asia WGS AF: 0.763 AC: 2655 AN: 3478

EpiCase AF: 0.756

EpiControl AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	0.85
Dann	Benign	0.31

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: rs13961; hg19: chr17-15207364; COSMIC: COSV58625938;