rs230897

chr17-15314072-G-Achr17-15314072-G-C

Variant summary

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

The NM_031898.3(TEKT3):c.878+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 1,613,520 control chromosomes in the GnomAD database, including 201,688 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 0.50 (19495 hom., cov: 32)
  • Exomes 𝑓: 0.50 (182193 hom.)
• Consequence: TEKT3 NM_031898.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.64

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT3	NM_031898.3	c.878+15C>T		intron_variant		ENST00000395930.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT3	ENST00000395930.6	c.878+15C>T		intron_variant		1	NM_031898.3	P1
TEKT3	ENST00000338696.6	c.878+15C>T		intron_variant		1		P1
TEKT3	ENST00000539245.5	c.380+15C>T		intron_variant		5
TEKT3	ENST00000395931.6	c.*178+15C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76489 AN: 151918 Hom.: 19473 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.480

GnomAD3 exomes AF: 0.492 AC: 123520 AN: 250930 Hom.: 30725 AF XY: 0.494 AC XY: 66968 AN XY: 135584

Gnomad AFR exome AF: 0.544

Gnomad AMR exome AF: 0.447

Gnomad ASJ exome AF: 0.412

Gnomad EAS exome AF: 0.577

Gnomad SAS exome AF: 0.527

Gnomad FIN exome AF: 0.509

Gnomad NFE exome AF: 0.481

Gnomad OTH exome AF: 0.472

GnomAD4 exome AF: 0.497 AC: 727048 AN: 1461482 Hom.: 182193 Cov.: 47 AF XY: 0.498 AC XY: 361888 AN XY: 727052

Gnomad4 AFR exome AF: 0.546

Gnomad4 AMR exome AF: 0.449

Gnomad4 ASJ exome AF: 0.412

Gnomad4 EAS exome AF: 0.564

Gnomad4 SAS exome AF: 0.526

Gnomad4 FIN exome AF: 0.504

Gnomad4 NFE exome AF: 0.496

Gnomad4 OTH exome AF: 0.495

GnomAD4 genome AF: 0.504 AC: 76561 AN: 152038 Hom.: 19495 Cov.: 32 AF XY: 0.504 AC XY: 37432 AN XY: 74312

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.479

Alfa AF: 0.474 Hom.: 17830

Bravo AF: 0.500

Asia WGS AF: 0.493 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.016
Dann	Benign	0.91

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: rs230897; hg19: chr17-15217389; COSMIC: COSV58625947; COSMIC: COSV58625947;