1-205150453-C-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.2467+227G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,938 control chromosomes in the GnomAD database, including 3,441 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (3441 hom., cov: 32)
• Consequence: DSTYK NM_015375.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.170

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=-0.85).
• BP6: Variant 1-205150453-C-T is Benign according to our data. Variant chr1-205150453-C-T is described in ClinVar as [Benign]. Clinvar id is 1240584.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSTYK	NM_015375.3	c.2467+227G>A		intron_variant		ENST00000367162.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSTYK	ENST00000367162.8	c.2467+227G>A		intron_variant		1	NM_015375.3	P1
DSTYK	ENST00000367161.7	c.2467+227G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28485 AN: 151820 Hom.: 3441 Cov.: 32

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.195

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.188 AC: 28491 AN: 151938 Hom.: 3441 Cov.: 32 AF XY: 0.193 AC XY: 14296 AN XY: 74234

Gnomad4 AFR AF: 0.0746

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.200

Alfa AF: 0.205 Hom.: 1696

Bravo AF: 0.189

Asia WGS AF: 0.442 AC: 1534 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	-0.85
Cadd	Benign	2.0
Dann	Benign	0.66

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: rs12120595; hg19: chr1-205119581; COSMIC: COSV65685862;