Variant 1-205147507-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015375.3(DSTYK):c.*51T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,562,506 control chromosomes in the GnomAD database, including 40,071 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3504 hom., cov: 31)

Exomes 𝑓: 0.21 ( 36567 hom. )

Consequence

DSTYK
NM_015375.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.94

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 1-205147507-A-T is Benign according to our data. Variant chr1-205147507-A-T is described in ClinVar as [Benign]. Clinvar id is 1244575.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 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.*51T>A		3_prime_UTR_variant	13/13	ENST00000367162.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSTYK	ENST00000367162.8 linkuse as main transcript	c.*51T>A		3_prime_UTR_variant	13/13	1	NM_015375.3	P1	Q6XUX3-1
DSTYK	ENST00000367161.7 linkuse as main transcript	c.*51T>A		3_prime_UTR_variant	12/12	1			Q6XUX3-2

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28617

AN:

152048

Hom.:

3503

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0746

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.270

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.515

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.195

GnomAD3 exomes

AF:

0.252

AC:

59011

AN:

234498

Hom.:

9005

AF XY:

0.255

AC XY:

32300

AN XY:

126896

show subpopulations

Gnomad AFR exome

AF:

0.0696

Gnomad AMR exome

AF:

0.346

Gnomad ASJ exome

AF:

0.189

Gnomad EAS exome

AF:

0.509

Gnomad SAS exome

AF:

0.360

Gnomad FIN exome

AF:

0.179

Gnomad NFE exome

AF:

0.199

Gnomad OTH exome

AF:

0.243

GnomAD4 exome

AF:

0.215

AC:

303076

AN:

1410338

Hom.:

36567

Cov.:

AF XY:

0.220

AC XY:

152818

AN XY:

695780

show subpopulations

Gnomad4 AFR exome

AF:

0.0676

Gnomad4 AMR exome

AF:

0.335

Gnomad4 ASJ exome

AF:

0.188

Gnomad4 EAS exome

AF:

0.499

Gnomad4 SAS exome

AF:

0.360

Gnomad4 FIN exome

AF:

0.182

Gnomad4 NFE exome

AF:

0.194

Gnomad4 OTH exome

AF:

0.232

GnomAD4 genome

AF:

0.188

AC:

28625

AN:

152168

Hom.:

3504

Cov.:

AF XY:

0.193

AC XY:

14391

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0745

Gnomad4 AMR

AF:

0.270

Gnomad4 ASJ

AF:

0.198

Gnomad4 EAS

AF:

0.515

Gnomad4 SAS

AF:

0.370

Gnomad4 FIN

AF:

0.170

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.201

Alfa

AF:

0.137

Hom.:

375

Bravo

AF:

0.189

Asia WGS

AF:

0.443

AC:

1537

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.87

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