Genetic Variant NM_031898.3:c.579+92C>T (chr17-15330915-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031898.3(TEKT3):c.579+92C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,310,438 control chromosomes in the GnomAD database, including 33,770 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 0.21 ( 3369 hom., cov: 32)

Exomes 𝑓: 0.23 ( 30401 hom. )

Consequence

TEKT3
NM_031898.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.276

Publications

3 publications found

Variant links:

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)

TEKT3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT3	NM_031898.3	MANE Select	c.579+92C>T		intron	N/A	NP_114104.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TEKT3	ENST00000395930.6	TSL:1 MANE Select	c.579+92C>T	intron	N/A	ENSP00000379263.1
TEKT3	ENST00000338696.6	TSL:1	c.579+92C>T	intron	N/A	ENSP00000343995.2
TEKT3	ENST00000539245.5	TSL:5	c.81+92C>T	intron	N/A	ENSP00000443280.1

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31451

AN:

151954

Hom.:

3365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.252

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.218

GnomAD4 exome

AF:

0.227

AC:

263011

AN:

1158366

Hom.:

30401

AF XY:

0.227

AC XY:

129079

AN XY:

568124

show subpopulations

African (AFR)

AF:

0.160

AC:

4104

AN:

25578

American (AMR)

AF:

0.160

AC:

3133

AN:

19596

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

4483

AN:

18124

East Asian (EAS)

AF:

0.260

AC:

8984

AN:

34492

South Asian (SAS)

AF:

0.219

AC:

12934

AN:

59092

European-Finnish (FIN)

AF:

0.202

AC:

8213

AN:

40738

Middle Eastern (MID)

AF:

0.247

AC:

1202

AN:

4866

European-Non Finnish (NFE)

AF:

0.230

AC:

208773

AN:

906684

Other (OTH)

AF:

0.227

AC:

11185

AN:

49196

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

10109

20217

30326

40434

50543

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7112

14224

21336

28448

35560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.207

AC:

31469

AN:

152072

Hom.:

3369

Cov.:

AF XY:

0.206

AC XY:

15334

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.164

AC:

6800

AN:

41472

American (AMR)

AF:

0.169

AC:

2577

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

890

AN:

3468

East Asian (EAS)

AF:

0.252

AC:

1306

AN:

5178

South Asian (SAS)

AF:

0.224

AC:

1079

AN:

4818

European-Finnish (FIN)

AF:

0.189

AC:

1998

AN:

10558

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.237

AC:

16132

AN:

67972

Other (OTH)

AF:

0.219

AC:

463

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1297

2593

3890

5186

6483

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.230

Hom.:

5271

Bravo

AF:

0.205

Asia WGS

AF:

0.228

AC:

790

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.46

(source)

DANN

Benign

0.31

PhyloP100

-0.28

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over