1-205147915-T-TA

Variant summary

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

The NM_015375.3(DSTYK):c.2603-171_2603-170insT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (18686 hom., cov: 0)
• Consequence: DSTYK NM_015375.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.28

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 1-205147915-T-TA is Benign according to our data. Variant chr1-205147915-T-TA is described in ClinVar as [Benign]. Clinvar id is 1220583.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSTYK	NM_015375.3	c.2603-171_2603-170insT		intron_variant		ENST00000367162.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSTYK	ENST00000367162.8	c.2603-171_2603-170insT		intron_variant		1	NM_015375.3	P1
DSTYK	ENST00000367161.7	c.2468-171_2468-170insT		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 69249 AN: 144280 Hom.: 18686 Cov.: 0

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.480 AC: 69264 AN: 144360 Hom.: 18686 Cov.: 0 AF XY: 0.477 AC XY: 33433 AN XY: 70104

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.511

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

May 11, 2021

- -

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: rs35284794; hg19: chr1-205117043;