1-205150434-GC-G

Position:

• chr1-205150434-GC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015375.3(DSTYK):​c.2467+245del 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 151,952 control chromosomes in the GnomAD database, including 3,451 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (3451 hom., cov: 28)
• Consequence: DSTYK NM_015375.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0320

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 -10 ACMG points.

• BP6: Variant 1-205150434-GC-G is Benign according to our data. Variant chr1-205150434-GC-G is described in ClinVar as [Benign]. Clinvar id is 1297990.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	Protein	UniProt
DSTYK	NM_015375.3	c.2467+245del		intron_variant		ENST00000367162.8	NP_056190.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSTYK	ENST00000367162.8	c.2467+245del		intron_variant		1	NM_015375.3	ENSP00000356130	P1
DSTYK	ENST00000367161.7	c.2467+245del		intron_variant		1		ENSP00000356129

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28505 AN: 151832 Hom.: 3451 Cov.: 28

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.270

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: 28511 AN: 151952 Hom.: 3451 Cov.: 28 AF XY: 0.193 AC XY: 14306 AN XY: 74262

Gnomad4 AFR AF: 0.0746

Gnomad4 AMR AF: 0.270

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: 0.0890 Hom.: 138

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

- -

Computational scores

Source: dbNSFP v4.3

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: rs67001092; hg19: chr1-205119562;