rs2305959

chr17-15330915-G-A

Variant summary

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

The NM_031898.3(TEKT3):c.579+92C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,310,438 control chromosomes in the GnomAD database, including 33,770 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 0.21 (3369 hom., cov: 32)
  • Exomes 𝑓: 0.23 (30401 hom.)
• Consequence: TEKT3 NM_031898.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT3	NM_031898.3	c.579+92C>T		intron_variant		ENST00000395930.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT3	ENST00000395930.6	c.579+92C>T		intron_variant		1	NM_031898.3	P1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31451 AN: 151954 Hom.: 3365 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.218

GnomAD4 exome AF: 0.227 AC: 263011 AN: 1158366 Hom.: 30401 AF XY: 0.227 AC XY: 129079 AN XY: 568124

Gnomad4 AFR exome AF: 0.160

Gnomad4 AMR exome AF: 0.160

Gnomad4 ASJ exome AF: 0.247

Gnomad4 EAS exome AF: 0.260

Gnomad4 SAS exome AF: 0.219

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.230

Gnomad4 OTH exome AF: 0.227

GnomAD4 genome AF: 0.207 AC: 31469 AN: 152072 Hom.: 3369 Cov.: 32 AF XY: 0.206 AC XY: 15334 AN XY: 74324

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.219

Alfa AF: 0.235 Hom.: 4149

Bravo AF: 0.205

Asia WGS AF: 0.228 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.46
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: rs2305959; hg19: chr17-15234232; COSMIC: COSV58628201; COSMIC: COSV58628201;