Variant chr2-218675520-CTT-C 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+67_434+68del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 1,095,578 control chromosomes in the GnomAD database, including 77 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.035 ( 55 hom., cov: 27)

Exomes 𝑓: 0.093 ( 22 hom. )

Consequence

STK36
NM_015690.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.12

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-CTT-C is Benign according to our data. Variant chr2-218675520-CTT-C is described in ClinVar as [Benign]. Clinvar id is 1280757.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.074 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.434+67_434+68del		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.434+67_434+68del	intron_variant	1	NM_015690.5	ENSP00000295709	P1	Q9NRP7-1
STK36	ENST00000392105.7 linkuse as main transcript	c.434+67_434+68del	intron_variant	1		ENSP00000375954		Q9NRP7-2
STK36	ENST00000424080.1 linkuse as main transcript	c.434+67_434+68del	intron_variant	5		ENSP00000403527
STK36	ENST00000440309.5 linkuse as main transcript	c.434+67_434+68del	intron_variant	5		ENSP00000394095	P1	Q9NRP7-1

Frequencies

GnomAD3 genomes

AF:

0.0352

AC:

4037

AN:

114706

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0353

Gnomad AMI

AF:

0.0254

Gnomad AMR

AF:

0.0206

Gnomad ASJ

AF:

0.0354

Gnomad EAS

AF:

0.0813

Gnomad SAS

AF:

0.0436

Gnomad FIN

AF:

0.0204

Gnomad MID

AF:

0.0238

Gnomad NFE

AF:

0.0360

Gnomad OTH

AF:

0.0360

GnomAD3 exomes

AF:

0.107

AC:

6325

AN:

59338

Hom.:

AF XY:

0.105

AC XY:

3283

AN XY:

31242

show subpopulations

Gnomad AFR exome

AF:

0.155

Gnomad AMR exome

AF:

0.116

Gnomad ASJ exome

AF:

0.0888

Gnomad EAS exome

AF:

0.143

Gnomad SAS exome

AF:

0.112

Gnomad FIN exome

AF:

0.0819

Gnomad NFE exome

AF:

0.0903

Gnomad OTH exome

AF:

0.0969

GnomAD4 exome

AF:

0.0932

AC:

91411

AN:

980870

Hom.:

AF XY:

0.0933

AC XY:

45254

AN XY:

485236

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.0962

Gnomad4 ASJ exome

AF:

0.0978

Gnomad4 EAS exome

AF:

0.122

Gnomad4 SAS exome

AF:

0.0980

Gnomad4 FIN exome

AF:

0.0964

Gnomad4 NFE exome

AF:

0.0901

Gnomad4 OTH exome

AF:

0.0976

GnomAD4 genome

AF:

0.0352

AC:

4037

AN:

114708

Hom.:

Cov.:

AF XY:

0.0338

AC XY:

1846

AN XY:

54690

show subpopulations

Gnomad4 AFR

AF:

0.0352

Gnomad4 AMR

AF:

0.0208

Gnomad4 ASJ

AF:

0.0354

Gnomad4 EAS

AF:

0.0813

Gnomad4 SAS

AF:

0.0435

Gnomad4 FIN

AF:

0.0204

Gnomad4 NFE

AF:

0.0360

Gnomad4 OTH

AF:

0.0358

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

May 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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