chr17-15314072-G-A

Variant names:

• chr17-15314072-G-A
• rs230897
• NM_031898.3:c.878+15C>T

Variant summary

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

The NM_031898.3(TEKT3):​c.878+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 1,613,520 control chromosomes in the GnomAD database, including 201,688 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 0.50 (19495 hom., cov: 32)
  • Exomes 𝑓: 0.50 (182193 hom.)
• Consequence: TEKT3 NM_031898.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.64
• Publications: 16 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031898.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT3	NM_031898.3	MANE Select	c.878+15C>T		intron	N/A	NP_114104.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT3	ENST00000395930.6	TSL:1 MANE Select	c.878+15C>T		intron	N/A	ENSP00000379263.1
	TEKT3	ENST00000338696.6	TSL:1	c.878+15C>T		intron	N/A	ENSP00000343995.2
	TEKT3	ENST00000539245.5	TSL:5	c.380+15C>T		intron	N/A	ENSP00000443280.1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76489 AN: 151918 Hom.: 19473 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.480

GnomAD2 exomes AF: 0.492 AC: 123520 AN: 250930 AF XY: 0.494

Gnomad AFR exome AF: 0.544

Gnomad AMR exome AF: 0.447

Gnomad ASJ exome AF: 0.412

Gnomad EAS exome AF: 0.577

Gnomad FIN exome AF: 0.509

Gnomad NFE exome AF: 0.481

Gnomad OTH exome AF: 0.472

GnomAD4 exome AF: 0.497 AC: 727048 AN: 1461482 Hom.: 182193 Cov.: 47 AF XY: 0.498 AC XY: 361888 AN XY: 727052

African (AFR) AF: 0.546 AC: 18267 AN: 33476

American (AMR) AF: 0.449 AC: 20084 AN: 44706

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 10769 AN: 26134

East Asian (EAS) AF: 0.564 AC: 22379 AN: 39696

South Asian (SAS) AF: 0.526 AC: 45379 AN: 86254

European-Finnish (FIN) AF: 0.504 AC: 26889 AN: 53396

Middle Eastern (MID) AF: 0.406 AC: 2341 AN: 5760

European-Non Finnish (NFE) AF: 0.496 AC: 551046 AN: 1111678

Other (OTH) AF: 0.495 AC: 29894 AN: 60382

GnomAD4 genome AF: 0.504 AC: 76561 AN: 152038 Hom.: 19495 Cov.: 32 AF XY: 0.504 AC XY: 37432 AN XY: 74312

African (AFR) AF: 0.544 AC: 22573 AN: 41482

American (AMR) AF: 0.458 AC: 6995 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3466

East Asian (EAS) AF: 0.577 AC: 2972 AN: 5150

South Asian (SAS) AF: 0.532 AC: 2564 AN: 4820

European-Finnish (FIN) AF: 0.518 AC: 5476 AN: 10568

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33043 AN: 67960

Other (OTH) AF: 0.479 AC: 1008 AN: 2104

Alfa AF: 0.478 Hom.: 23371

Bravo AF: 0.500

Asia WGS AF: 0.493 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.016
DANN	Benign	0.91
PhyloP100		-3.6
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: rs230897; hg19: chr17-15217389; COSMIC: COSV58625947; COSMIC: COSV58625947;