Variant chr1-205160191-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_015375.3(DSTYK):c.2028C>T(p.Phe676=) 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

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DSTYK	NM_015375.3 linkuse as main transcript	c.2028C>T	p.Phe676=	synonymous_variant	8/13	ENST00000367162.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSTYK	ENST00000367162.8 linkuse as main transcript	c.2028C>T	p.Phe676=	synonymous_variant	8/13	1	NM_015375.3	P1	Q6XUX3-1
DSTYK	ENST00000367161.7 linkuse as main transcript	c.2028C>T	p.Phe676=	synonymous_variant	8/12	1			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

GnomAD3 exomes

AF:

0.303

AC:

76058

AN:

251378

Hom.:

12152

AF XY:

0.301

AC XY:

40854

AN XY:

135848

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 SAS exome

AF:

0.412

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

Gnomad4 AFR exome

AF:

0.374

Gnomad4 AMR exome

AF:

0.341

Gnomad4 ASJ exome

AF:

0.289

Gnomad4 EAS exome

AF:

0.406

Gnomad4 SAS exome

AF:

0.406

Gnomad4 FIN exome

AF:

0.311

Gnomad4 NFE exome

AF:

0.234

Gnomad4 OTH exome

AF:

0.277

GnomAD4 genome

AF:

0.300

AC:

45517

AN:

151972

Hom.:

7249

Cov.:

AF XY:

0.305

AC XY:

22670

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.377

Gnomad4 AMR

AF:

0.315

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.398

Gnomad4 SAS

AF:

0.412

Gnomad4 FIN

AF:

0.313

Gnomad4 NFE

AF:

0.232

Gnomad4 OTH

AF:

0.300

Alfa

AF:

0.260

Hom.:

3758

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

Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 13, 2020	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Congenital anomalies of kidney and urinary tract 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

Hereditary spastic paraplegia 23

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

8.2

DANN

Benign

0.79

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over