chr17-15341610-A-T

Variant names:

• chr17-15341610-A-T
• rs396445
• ENST00000539316.1:c.-122T>A

Variant summary

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

The ENST00000539316.1(TEKT3):​c.-122T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,236 control chromosomes in the GnomAD database, including 1,125 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 0.11 (1125 hom., cov: 33)
  • Exomes 𝑓: 0.079 (0 hom.)
• Consequence: TEKT3 ENST00000539316.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• 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)

ENSG00000298674 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKT3	NM_031898.3	c.-156T>A		upstream_gene_variant		ENST00000395930.6	NP_114104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEKT3	ENST00000395930.6	c.-156T>A		upstream_gene_variant		1	NM_031898.3	ENSP00000379263.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16684 AN: 152080 Hom.: 1122 Cov.: 33

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.107

GnomAD4 exome AF: 0.0789 AC: 3 AN: 38 Hom.: 0 Cov.: 0 AF XY: 0.0385 AC XY: 1 AN XY: 26

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0714 AC: 2 AN: 28

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.110 AC: 16695 AN: 152198 Hom.: 1125 Cov.: 33 AF XY: 0.112 AC XY: 8334 AN XY: 74402

African (AFR) AF: 0.0426 AC: 1772 AN: 41580

American (AMR) AF: 0.154 AC: 2355 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1101 AN: 5114

South Asian (SAS) AF: 0.161 AC: 775 AN: 4824

European-Finnish (FIN) AF: 0.140 AC: 1485 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8378 AN: 67980

Other (OTH) AF: 0.104 AC: 220 AN: 2110

Alfa AF: 0.118 Hom.: 133

Bravo AF: 0.109

Asia WGS AF: 0.188 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.44
DANN	Benign	0.42
PhyloP100		-3.0
PromoterAI		-0.22	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs396445; hg19: chr17-15244927;