rs2286516

chr17-15312343-T-C

Variant summary

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

The NM_031898.3(TEKT3):c.1017A>G(p.Gln339=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,613,950 control chromosomes in the GnomAD database, including 55,434 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 0.24 (4670 hom., cov: 33)
  • Exomes 𝑓: 0.26 (50764 hom.)
• Consequence: TEKT3 NM_031898.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP7: Synonymous conserved (PhyloP=0.648 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT3	NM_031898.3	c.1017A>G	p.Gln339=	synonymous_variant	7/9	ENST00000395930.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT3	ENST00000395930.6	c.1017A>G	p.Gln339=	synonymous_variant	7/9	1	NM_031898.3	P1
TEKT3	ENST00000338696.6	c.1017A>G	p.Gln339=	synonymous_variant	5/7	1		P1
TEKT3	ENST00000539245.5	c.519A>G	p.Gln173=	synonymous_variant	8/8	5
TEKT3	ENST00000395931.6	c.*317A>G		3_prime_UTR_variant, NMD_transcript_variant	5/8	5

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36505 AN: 152078 Hom.: 4667 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.250

GnomAD3 exomes AF: 0.273 AC: 68590 AN: 251434 Hom.: 9553 AF XY: 0.273 AC XY: 37149 AN XY: 135880

Gnomad AFR exome AF: 0.160

Gnomad AMR exome AF: 0.328

Gnomad ASJ exome AF: 0.326

Gnomad EAS exome AF: 0.256

Gnomad SAS exome AF: 0.278

Gnomad FIN exome AF: 0.282

Gnomad NFE exome AF: 0.267

Gnomad OTH exome AF: 0.271

GnomAD4 exome AF: 0.261 AC: 381614 AN: 1461754 Hom.: 50764 Cov.: 35 AF XY: 0.262 AC XY: 190418 AN XY: 727176

Gnomad4 AFR exome AF: 0.160

Gnomad4 AMR exome AF: 0.318

Gnomad4 ASJ exome AF: 0.327

Gnomad4 EAS exome AF: 0.272

Gnomad4 SAS exome AF: 0.277

Gnomad4 FIN exome AF: 0.287

Gnomad4 NFE exome AF: 0.257

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome AF: 0.240 AC: 36508 AN: 152196 Hom.: 4670 Cov.: 33 AF XY: 0.242 AC XY: 18029 AN XY: 74406

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.252

Alfa AF: 0.262 Hom.: 8645

Bravo AF: 0.237

Asia WGS AF: 0.308 AC: 1072 AN: 3478

EpiCase AF: 0.267

EpiControl AF: 0.277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	4.4
Dann	Benign	0.64

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: rs2286516; hg19: chr17-15215660; COSMIC: COSV58626360; COSMIC: COSV58626360;