Variant chr2-218675520-C-CT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_015690.5(STK36):c.434+68dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0605 in 1,130,330 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 1 hom., cov: 27)

Exomes 𝑓: 0.067 ( 3 hom. )

Consequence

STK36
NM_015690.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0100

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 -10 ACMG points.

BP6

Variant 2-218675520-C-CT is Benign according to our data. Variant chr2-218675520-C-CT is described in ClinVar as [Benign]. Clinvar id is 1272769.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.069 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.434+68dup		intron_variant		ENST00000295709.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
STK36	ENST00000295709.8 linkuse as main transcript	c.434+68dup	intron_variant	1	NM_015690.5	P1	Q9NRP7-1
STK36	ENST00000392105.7 linkuse as main transcript	c.434+68dup	intron_variant	1			Q9NRP7-2
STK36	ENST00000424080.1 linkuse as main transcript	c.434+68dup	intron_variant	5
STK36	ENST00000440309.5 linkuse as main transcript	c.434+68dup	intron_variant	5		P1	Q9NRP7-1

Frequencies

GnomAD3 genomes

AF:

0.00542

AC:

622

AN:

114790

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00454

Gnomad AMI

AF:

0.00668

Gnomad AMR

AF:

0.00228

Gnomad ASJ

AF:

0.00986

Gnomad EAS

AF:

0.00781

Gnomad SAS

AF:

0.00363

Gnomad FIN

AF:

0.00207

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00664

Gnomad OTH

AF:

0.00315

GnomAD3 exomes

AF:

0.0516

AC:

3064

AN:

59338

Hom.:

AF XY:

0.0486

AC XY:

1517

AN XY:

31242

show subpopulations

Gnomad AFR exome

AF:

0.0333

Gnomad AMR exome

AF:

0.0663

Gnomad ASJ exome

AF:

0.0549

Gnomad EAS exome

AF:

0.0690

Gnomad SAS exome

AF:

0.0533

Gnomad FIN exome

AF:

0.0165

Gnomad NFE exome

AF:

0.0488

Gnomad OTH exome

AF:

0.0591

GnomAD4 exome

AF:

0.0668

AC:

67802

AN:

1015538

Hom.:

Cov.:

AF XY:

0.0664

AC XY:

33413

AN XY:

503256

show subpopulations

Gnomad4 AFR exome

AF:

0.0295

Gnomad4 AMR exome

AF:

0.0585

Gnomad4 ASJ exome

AF:

0.0678

Gnomad4 EAS exome

AF:

0.0575

Gnomad4 SAS exome

AF:

0.0709

Gnomad4 FIN exome

AF:

0.0532

Gnomad4 NFE exome

AF:

0.0684

Gnomad4 OTH exome

AF:

0.0648

GnomAD4 genome

AF:

0.00542

AC:

622

AN:

114792

Hom.:

Cov.:

AF XY:

0.00523

AC XY:

286

AN XY:

54722

show subpopulations

Gnomad4 AFR

AF:

0.00453

Gnomad4 AMR

AF:

0.00228

Gnomad4 ASJ

AF:

0.00986

Gnomad4 EAS

AF:

0.00784

Gnomad4 SAS

AF:

0.00364

Gnomad4 FIN

AF:

0.00207

Gnomad4 NFE

AF:

0.00664

Gnomad4 OTH

AF:

0.00313

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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