rs1062715

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_015375.3(DSTYK):c.2028C>T(p.Phe676Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,613,754 control chromosomes in the GnomAD database, including 59,531 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7249 hom., cov: 32)

Exomes 𝑓: 0.26 ( 52282 hom. )

Consequence

DSTYK
NM_015375.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 2.66

Publications

17 publications found

Variant links:

Genes affected

DSTYK (HGNC:29043): (dual serine/threonine and tyrosine protein kinase) This gene encodes a dual serine/threonine and tyrosine protein kinase which is expressed in multiple tissues. It is thought to function as a regulator of cell death. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

DSTYK Gene-Disease associations (from GenCC):

congenital anomalies of kidney and urinary tract 1
Inheritance: AD, AR Classification: DEFINITIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
hereditary spastic paraplegia 23
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: G2P, Orphanet
complex hereditary spastic paraplegia
Inheritance: AR Classification: MODERATE Submitted by: ClinGen
renal agenesis, unilateral
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

DSTYK links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 1-205160191-G-A is Benign according to our data. Variant chr1-205160191-G-A is described in ClinVar as [Benign]. Clinvar id is 260658.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.66 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSTYK	NM_015375.3 link	c.2028C>T	p.Phe676Phe	synonymous_variant	Exon 8 of 13	ENST00000367162.8	NP_056190.1	Q6XUX3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSTYK	ENST00000367162.8 link	c.2028C>T	p.Phe676Phe	synonymous_variant	Exon 8 of 13	1	NM_015375.3	ENSP00000356130.3		Q6XUX3-1
DSTYK	ENST00000367161.7 link	c.2028C>T	p.Phe676Phe	synonymous_variant	Exon 8 of 12	1		ENSP00000356129.3		Q6XUX3-2

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45484

AN:

151854

Hom.:

7241

Cov.:

show subpopulations

Gnomad AFR

AF:

0.377

Gnomad AMI

AF:

0.312

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.413

Gnomad FIN

AF:

0.313

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.300

GnomAD2 exomes

AF:

0.303

AC:

76058

AN:

251378

AF XY:

0.301

show subpopulations

Gnomad AFR exome

AF:

0.385

Gnomad AMR exome

AF:

0.339

Gnomad ASJ exome

AF:

0.288

Gnomad EAS exome

AF:

0.415

Gnomad FIN exome

AF:

0.314

Gnomad NFE exome

AF:

0.233

Gnomad OTH exome

AF:

0.261

GnomAD4 exome

AF:

0.261

AC:

381723

AN:

1461782

Hom.:

52282

Cov.:

AF XY:

0.264

AC XY:

192092

AN XY:

727194

show subpopulations

African (AFR)

AF:

0.374

AC:

12530

AN:

33480

American (AMR)

AF:

0.341

AC:

15258

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.289

AC:

7544

AN:

26134

East Asian (EAS)

AF:

0.406

AC:

16132

AN:

39698

South Asian (SAS)

AF:

0.406

AC:

35059

AN:

86254

European-Finnish (FIN)

AF:

0.311

AC:

16601

AN:

53420

Middle Eastern (MID)

AF:

0.240

AC:

1384

AN:

5762

European-Non Finnish (NFE)

AF:

0.234

AC:

260469

AN:

1111924

Other (OTH)

AF:

0.277

AC:

16746

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

16431

32863

49294

65726

82157

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.300

AC:

45517

AN:

151972

Hom.:

7249

Cov.:

AF XY:

0.305

AC XY:

22670

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.377

AC:

15605

AN:

41444

American (AMR)

AF:

0.315

AC:

4808

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

1021

AN:

3470

East Asian (EAS)

AF:

0.398

AC:

2050

AN:

5148

South Asian (SAS)

AF:

0.412

AC:

1984

AN:

4814

European-Finnish (FIN)

AF:

0.313

AC:

3305

AN:

10546

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.232

AC:

15749

AN:

67966

Other (OTH)

AF:

0.300

AC:

633

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1572

3144

4716

6288

7860

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.262

Hom.:

4206

Bravo

AF:

0.306

Asia WGS

AF:

0.393

AC:

1364

AN:

3478

EpiCase

AF:

0.236

EpiControl

AF:

0.227

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 13, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Congenital anomalies of kidney and urinary tract 1

Benign:1

Jul 30, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hereditary spastic paraplegia 23

Benign:1

Jul 30, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

8.2

(source)

DANN

Benign

0.79

PhyloP100

2.7

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs1062715

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over