Variant rs2303565 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_015690.5(STK36):c.1137-17T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,603,632 control chromosomes in the GnomAD database, including 171,418 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 25604 hom., cov: 31)

Exomes 𝑓: 0.44 ( 145814 hom. )

Consequence

STK36
NM_015690.5 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.00

Variant links:

Genes affected

STK36 (HGNC:17209): (serine/threonine kinase 36) This gene encodes a member of the serine/threonine kinase family of enzymes. This family member is similar to a Drosophila protein that plays a key role in the Hedgehog signaling pathway. This human protein is a positive regulator of the GLI zinc-finger transcription factors. Knockout studies of the homologous mouse gene suggest that defects in this human gene may lead to congenital hydrocephalus, possibly due to a functional defect in motile cilia. Because Hedgehog signaling is frequently activated in certain kinds of gastrointestinal cancers, it has been suggested that this gene is a target for the treatment of these cancers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]

STK36 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 2-218680586-T-C is Benign according to our data. Variant chr2-218680586-T-C is described in ClinVar as [Benign]. Clinvar id is 1265137.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK36	NM_015690.5 linkuse as main transcript	c.1137-17T>C		splice_polypyrimidine_tract_variant, intron_variant		ENST00000295709.8	NP_056505.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
STK36	ENST00000295709.8 linkuse as main transcript	c.1137-17T>C	splice_polypyrimidine_tract_variant, intron_variant	1	NM_015690.5	ENSP00000295709	P1	Q9NRP7-1
STK36	ENST00000392105.7 linkuse as main transcript	c.1137-17T>C	splice_polypyrimidine_tract_variant, intron_variant	1		ENSP00000375954		Q9NRP7-2
STK36	ENST00000440309.5 linkuse as main transcript	c.1137-17T>C	splice_polypyrimidine_tract_variant, intron_variant	5		ENSP00000394095	P1	Q9NRP7-1
STK36	ENST00000414413.5 linkuse as main transcript	c.32-17T>C	splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant	5		ENSP00000406184

Frequencies

GnomAD3 genomes

AF:

0.543

AC:

82513

AN:

151898

Hom.:

25539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.854

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.465

Gnomad ASJ

AF:

0.414

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.327

Gnomad FIN

AF:

0.436

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.445

Gnomad OTH

AF:

0.506

GnomAD3 exomes

AF:

0.425

AC:

100411

AN:

236130

Hom.:

23591

AF XY:

0.417

AC XY:

52975

AN XY:

127082

show subpopulations

Gnomad AFR exome

AF:

0.864

Gnomad AMR exome

AF:

0.410

Gnomad ASJ exome

AF:

0.405

Gnomad EAS exome

AF:

0.136

Gnomad SAS exome

AF:

0.336

Gnomad FIN exome

AF:

0.443

Gnomad NFE exome

AF:

0.439

Gnomad OTH exome

AF:

0.441

GnomAD4 exome

AF:

0.439

AC:

636921

AN:

1451616

Hom.:

145814

Cov.:

AF XY:

0.434

AC XY:

312860

AN XY:

721228

show subpopulations

Gnomad4 AFR exome

AF:

0.875

Gnomad4 AMR exome

AF:

0.416

Gnomad4 ASJ exome

AF:

0.410

Gnomad4 EAS exome

AF:

0.129

Gnomad4 SAS exome

AF:

0.337

Gnomad4 FIN exome

AF:

0.441

Gnomad4 NFE exome

AF:

0.446

Gnomad4 OTH exome

AF:

0.448

GnomAD4 genome

AF:

0.544

AC:

82637

AN:

152016

Hom.:

25604

Cov.:

AF XY:

0.535

AC XY:

39726

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.854

Gnomad4 AMR

AF:

0.465

Gnomad4 ASJ

AF:

0.414

Gnomad4 EAS

AF:

0.138

Gnomad4 SAS

AF:

0.328

Gnomad4 FIN

AF:

0.436

Gnomad4 NFE

AF:

0.445

Gnomad4 OTH

AF:

0.505

Alfa

AF:

0.454

Hom.:

11229

Bravo

AF:

0.561

Asia WGS

AF:

0.293

AC:

1023

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.1

DANN

Benign

0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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