rs230901

Positions:

• chr17-15327949-A-G

Variant summary

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

The ENST00000395930.6(TEKT3):​c.663+43T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,553,806 control chromosomes in the GnomAD database, including 10,286 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 0.098 (861 hom., cov: 33)
  • Exomes 𝑓: 0.11 (9425 hom.)
• Consequence: TEKT3 ENST00000395930.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEKT3	NM_031898.3	c.663+43T>C		intron_variant		ENST00000395930.6	NP_114104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEKT3	ENST00000395930.6	c.663+43T>C		intron_variant		1	NM_031898.3	ENSP00000379263	P1

Frequencies

GnomAD3 genomes AF: 0.0979 AC: 14900 AN: 152140 Hom.: 862 Cov.: 33

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0923

GnomAD3 exomes AF: 0.122 AC: 30649 AN: 250582 Hom.: 2132 AF XY: 0.122 AC XY: 16548 AN XY: 135436

Gnomad AFR exome AF: 0.0506

Gnomad AMR exome AF: 0.169

Gnomad ASJ exome AF: 0.0939

Gnomad EAS exome AF: 0.220

Gnomad SAS exome AF: 0.146

Gnomad FIN exome AF: 0.103

Gnomad NFE exome AF: 0.103

Gnomad OTH exome AF: 0.107

GnomAD4 exome AF: 0.111 AC: 155456 AN: 1401548 Hom.: 9425 Cov.: 22 AF XY: 0.112 AC XY: 78140 AN XY: 700074

Gnomad4 AFR exome AF: 0.0497

Gnomad4 AMR exome AF: 0.165

Gnomad4 ASJ exome AF: 0.0915

Gnomad4 EAS exome AF: 0.206

Gnomad4 SAS exome AF: 0.146

Gnomad4 FIN exome AF: 0.104

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.107

GnomAD4 genome AF: 0.0979 AC: 14912 AN: 152258 Hom.: 861 Cov.: 33 AF XY: 0.0985 AC XY: 7333 AN XY: 74450

Gnomad4 AFR AF: 0.0521

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0984 Hom.: 169

Bravo AF: 0.0983

Asia WGS AF: 0.189 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs230901; hg19: chr17-15231266; COSMIC: COSV58625965; COSMIC: COSV58625965;