17-15322326-A-T

Variant names:

• chr17-15322326-A-T
• rs433068
• NM_031898.3:c.664-3179T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031898.3(TEKT3):​c.664-3179T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,250 control chromosomes in the GnomAD database, including 1,891 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 0.15 (1891 hom., cov: 32)
• Consequence: TEKT3 NM_031898.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 3 publications found

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]

TEKT3 Gene-Disease associations (from GenCC):

• spermatogenic failure 81

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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 rank	MANE	Protein	UniProt
TEKT3	NM_031898.3	c.664-3179T>A		intron_variant	Intron 4 of 8	ENST00000395930.6	NP_114104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEKT3	ENST00000395930.6	c.664-3179T>A		intron_variant	Intron 4 of 8	1	NM_031898.3	ENSP00000379263.1
TEKT3	ENST00000338696.6	c.664-3179T>A		intron_variant	Intron 2 of 6	1		ENSP00000343995.2
TEKT3	ENST00000539245.5	c.166-3179T>A		intron_variant	Intron 5 of 7	5		ENSP00000443280.1
TEKT3	ENST00000395931.6	n.663+5666T>A		intron_variant	Intron 3 of 7	5		ENSP00000379264.2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23263 AN: 152132 Hom.: 1878 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.146

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.153 AC: 23316 AN: 152250 Hom.: 1891 Cov.: 32 AF XY: 0.152 AC XY: 11280 AN XY: 74428

African (AFR) AF: 0.200 AC: 8307 AN: 41532

American (AMR) AF: 0.175 AC: 2680 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1129 AN: 5180

South Asian (SAS) AF: 0.165 AC: 798 AN: 4822

European-Finnish (FIN) AF: 0.108 AC: 1141 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8451 AN: 68012

Other (OTH) AF: 0.148 AC: 312 AN: 2110

Alfa AF: 0.0569 Hom.: 47

Bravo AF: 0.163

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.75
PhyloP100		0.062
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs433068; hg19: chr17-15225643;