Variant chr2-218674076-A-C 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.303+120A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 943,152 control chromosomes in the GnomAD database, including 59,047 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 7492 hom., cov: 32)

Exomes 𝑓: 0.35 ( 51555 hom. )

Consequence

STK36
NM_015690.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.34

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=-0.79).

BP6

Variant 2-218674076-A-C is Benign according to our data. Variant chr2-218674076-A-C is described in ClinVar as [Benign]. Clinvar id is 1268211.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK36	NM_015690.5 linkuse as main transcript	c.303+120A>C		intron_variant		ENST00000295709.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK36	ENST00000295709.8 linkuse as main transcript	c.303+120A>C		intron_variant		1	NM_015690.5	P1	Q9NRP7-1

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

42293

AN:

152028

Hom.:

7492

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0699

Gnomad AMI

AF:

0.358

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.0614

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.399

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.386

Gnomad OTH

AF:

0.282

GnomAD4 exome

AF:

0.348

AC:

275324

AN:

791006

Hom.:

51555

AF XY:

0.346

AC XY:

140435

AN XY:

405884

show subpopulations

Gnomad4 AFR exome

AF:

0.0634

Gnomad4 AMR exome

AF:

0.343

Gnomad4 ASJ exome

AF:

0.345

Gnomad4 EAS exome

AF:

0.0617

Gnomad4 SAS exome

AF:

0.277

Gnomad4 FIN exome

AF:

0.394

Gnomad4 NFE exome

AF:

0.381

Gnomad4 OTH exome

AF:

0.327

GnomAD4 genome

AF:

0.278

AC:

42292

AN:

152146

Hom.:

7492

Cov.:

AF XY:

0.277

AC XY:

20567

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.0697

Gnomad4 AMR

AF:

0.335

Gnomad4 ASJ

AF:

0.351

Gnomad4 EAS

AF:

0.0619

Gnomad4 SAS

AF:

0.271

Gnomad4 FIN

AF:

0.399

Gnomad4 NFE

AF:

0.386

Gnomad4 OTH

AF:

0.283

Alfa

AF:

0.326

Hom.:

1123

Bravo

AF:

0.266

Asia WGS

AF:

0.178

AC:

620

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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