1-205147507-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.94

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]

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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	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	c.*51T>A		3_prime_UTR_variant	13/13	1	NM_015375.3	P1
DSTYK	ENST00000367161.7	c.*51T>A		3_prime_UTR_variant	12/12	1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28617 AN: 152048 Hom.: 3503 Cov.: 31

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

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.: 27 AF XY: 0.220 AC XY: 152818 AN XY: 695780

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.: 31 AF XY: 0.193 AC XY: 14391 AN XY: 74394

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	17
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

Other links and lift over

dbSNP: rs11367; hg19: chr1-205116635; COSMIC: COSV65685860;