Genetic Variant TEKT5:c.564+38C>A (chr16-10694272-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_144674.2(TEKT5):c.564+38C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 1,517,134 control chromosomes in the GnomAD database, including 222,264 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 0.57 ( 25595 hom., cov: 32)

Exomes 𝑓: 0.53 ( 196669 hom. )

Consequence

TEKT5
NM_144674.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.69

Publications

10 publications found

Variant links:

Genes affected

TEKT5 (HGNC:26554): (tektin 5) Predicted to be involved in cilium assembly and cilium movement involved in cell motility. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TEKT5 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144674.2. 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
	TEKT5	NM_144674.2	MANE Select	c.564+38C>A		intron	N/A	NP_653275.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT5	ENST00000283025.7	TSL:1 MANE Select	c.564+38C>A		intron	N/A	ENSP00000283025.2

Frequencies

GnomAD3 genomes

AF:

0.575

AC:

87271

AN:

151872

Hom.:

25567

Cov.:

show subpopulations

Gnomad AFR

AF:

0.677

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.609

Gnomad ASJ

AF:

0.446

Gnomad EAS

AF:

0.621

Gnomad SAS

AF:

0.508

Gnomad FIN

AF:

0.552

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.541

GnomAD2 exomes

AF:

0.557

AC:

101500

AN:

182140

AF XY:

0.546

show subpopulations

Gnomad AFR exome

AF:

0.681

Gnomad AMR exome

AF:

0.673

Gnomad ASJ exome

AF:

0.425

Gnomad EAS exome

AF:

0.614

Gnomad FIN exome

AF:

0.559

Gnomad NFE exome

AF:

0.513

Gnomad OTH exome

AF:

0.520

GnomAD4 exome

AF:

0.535

AC:

730153

AN:

1365144

Hom.:

196669

Cov.:

AF XY:

0.533

AC XY:

356252

AN XY:

668898

show subpopulations

African (AFR)

AF:

0.680

AC:

20810

AN:

30584

American (AMR)

AF:

0.666

AC:

20674

AN:

31056

Ashkenazi Jewish (ASJ)

AF:

0.423

AC:

8671

AN:

20488

East Asian (EAS)

AF:

0.609

AC:

23656

AN:

38824

South Asian (SAS)

AF:

0.503

AC:

36095

AN:

71808

European-Finnish (FIN)

AF:

0.561

AC:

25148

AN:

44844

Middle Eastern (MID)

AF:

0.404

AC:

2156

AN:

5332

European-Non Finnish (NFE)

AF:

0.529

AC:

563369

AN:

1065844

Other (OTH)

AF:

0.525

AC:

29574

AN:

56364

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

18275

36550

54824

73099

91374

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16880

33760

50640

67520

84400

<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:

0.575

AC:

87351

AN:

151990

Hom.:

25595

Cov.:

AF XY:

0.576

AC XY:

42774

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.677

AC:

28041

AN:

41448

American (AMR)

AF:

0.609

AC:

9310

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.446

AC:

1544

AN:

3464

East Asian (EAS)

AF:

0.621

AC:

3203

AN:

5158

South Asian (SAS)

AF:

0.507

AC:

2443

AN:

4818

European-Finnish (FIN)

AF:

0.552

AC:

5817

AN:

10538

Middle Eastern (MID)

AF:

0.476

AC:

140

AN:

294

European-Non Finnish (NFE)

AF:

0.521

AC:

35418

AN:

67970

Other (OTH)

AF:

0.546

AC:

1154

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1901

3803

5704

7606

9507

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

734

1468

2202

2936

3670

<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:

0.471

Hom.:

3089

Bravo

AF:

0.581

Asia WGS

AF:

0.565

AC:

1968

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.50

(source)

DANN

Benign

0.51

PhyloP100

-3.7

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