Genetic Variant NM_004760.3:c.*344C>T (chr7-43625186-C-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_004760.3(STK17A):c.*344C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 189,902 control chromosomes in the GnomAD database, including 46,933 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 0.71 ( 38677 hom., cov: 32)

Exomes 𝑓: 0.65 ( 8256 hom. )

Consequence

STK17A
NM_004760.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.385

Publications

11 publications found

Variant links:

Genes affected

STK17A (HGNC:11395): (serine/threonine kinase 17a) This gene is a member of the DAP kinase-related apoptosis-inducing protein kinase family and encodes an autophosphorylated nuclear protein with a protein kinase domain. The protein has apoptosis-inducing activity. [provided by RefSeq, Jul 2008]

STK17A links:

COA1 (HGNC:21868): (cytochrome c oxidase assembly factor 1) Involved in mitochondrial cytochrome c oxidase assembly and mitochondrial respiratory chain complex I assembly. Located in cytosol and mitochondrion. Is integral component of mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

COA1 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=-0.68).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK17A	NM_004760.3 link	c.*344C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000319357.6	NP_004751.2	Q9UEE5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK17A	ENST00000319357.6 link	c.*344C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_004760.3	ENSP00000319192.5		Q9UEE5

Frequencies

GnomAD3 genomes

AF:

0.708

AC:

107681

AN:

152028

Hom.:

38640

Cov.:

show subpopulations

Gnomad AFR

AF:

0.838

Gnomad AMI

AF:

0.580

Gnomad AMR

AF:

0.663

Gnomad ASJ

AF:

0.693

Gnomad EAS

AF:

0.588

Gnomad SAS

AF:

0.760

Gnomad FIN

AF:

0.664

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.655

Gnomad OTH

AF:

0.678

GnomAD4 exome

AF:

0.655

AC:

24726

AN:

37756

Hom.:

8256

Cov.:

AF XY:

0.658

AC XY:

12618

AN XY:

19184

show subpopulations

African (AFR)

AF:

0.825

AC:

713

AN:

864

American (AMR)

AF:

0.617

AC:

1598

AN:

2588

Ashkenazi Jewish (ASJ)

AF:

0.692

AC:

852

AN:

1232

East Asian (EAS)

AF:

0.563

AC:

1184

AN:

2104

South Asian (SAS)

AF:

0.755

AC:

2444

AN:

3238

European-Finnish (FIN)

AF:

0.671

AC:

929

AN:

1384

Middle Eastern (MID)

AF:

0.783

AC:

130

AN:

166

European-Non Finnish (NFE)

AF:

0.643

AC:

15349

AN:

23872

Other (OTH)

AF:

0.662

AC:

1527

AN:

2308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

405

810

1216

1621

2026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

138

276

414

552

690

<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:

0.708

AC:

107780

AN:

152146

Hom.:

38677

Cov.:

AF XY:

0.706

AC XY:

52521

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.838

AC:

34820

AN:

41536

American (AMR)

AF:

0.663

AC:

10135

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.693

AC:

2404

AN:

3468

East Asian (EAS)

AF:

0.589

AC:

3049

AN:

5176

South Asian (SAS)

AF:

0.760

AC:

3672

AN:

4830

European-Finnish (FIN)

AF:

0.664

AC:

7008

AN:

10554

Middle Eastern (MID)

AF:

0.718

AC:

211

AN:

294

European-Non Finnish (NFE)

AF:

0.655

AC:

44525

AN:

67974

Other (OTH)

AF:

0.676

AC:

1428

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1603

3205

4808

6410

8013

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

830

1660

2490

3320

4150

<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:

0.670

Hom.:

12335

Bravo

AF:

0.709

Asia WGS

AF:

0.658

AC:

2288

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

6.4

(source)

DANN

Benign

0.75

PhyloP100

-0.39

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over