17-15319218-CA-CAA

Position:

• chr17-15319218-CA-CAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_031898.3(TEKT3):​c.664-72_664-71insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 1,310,716 control chromosomes in the GnomAD database, including 250,176 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.65 (32486 hom., cov: 0)
  • Exomes 𝑓: 0.61 (217690 hom.)
• Consequence: TEKT3 NM_031898.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT3	NM_031898.3	c.664-72_664-71insT		intron_variant		ENST00000395930.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT3	ENST00000395930.6	c.664-72_664-71insT		intron_variant		1	NM_031898.3	P1
TEKT3	ENST00000338696.6	c.664-72_664-71insT		intron_variant		1		P1
TEKT3	ENST00000539245.5	c.166-72_166-71insT		intron_variant		5
TEKT3	ENST00000395931.6	c.664-4940_664-4939insT		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98828 AN: 151922 Hom.: 32464 Cov.: 0

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.656

GnomAD4 exome AF: 0.607 AC: 703369 AN: 1158676 Hom.: 217690 AF XY: 0.608 AC XY: 352191 AN XY: 579464

Gnomad4 AFR exome AF: 0.725

Gnomad4 AMR exome AF: 0.715

Gnomad4 ASJ exome AF: 0.675

Gnomad4 EAS exome AF: 0.765

Gnomad4 SAS exome AF: 0.639

Gnomad4 FIN exome AF: 0.544

Gnomad4 NFE exome AF: 0.593

Gnomad4 OTH exome AF: 0.615

GnomAD4 genome AF: 0.650 AC: 98899 AN: 152040 Hom.: 32486 Cov.: 0 AF XY: 0.650 AC XY: 48316 AN XY: 74326

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.655

Alfa AF: 0.617 Hom.: 3509

Bravo AF: 0.666

Asia WGS AF: 0.753 AC: 2617 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11387328; hg19: chr17-15222535;