Variant chr2-218675520-CT-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+68del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 114,796 control chromosomes in the GnomAD database, including 1,176 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.091 ( 1176 hom., cov: 27)

Exomes 𝑓: 0.25 ( 51 hom. )

Failed GnomAD Quality Control

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-218675520-CT-C is Benign according to our data. Variant chr2-218675520-CT-C is described in ClinVar as [Benign]. Clinvar id is 1178774.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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+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+68del	intron_variant	1	NM_015690.5	ENSP00000295709	P1	Q9NRP7-1
STK36	ENST00000392105.7 linkuse as main transcript	c.434+68del	intron_variant	1		ENSP00000375954		Q9NRP7-2
STK36	ENST00000424080.1 linkuse as main transcript	c.434+68del	intron_variant	5		ENSP00000403527
STK36	ENST00000440309.5 linkuse as main transcript	c.434+68del	intron_variant	5		ENSP00000394095	P1	Q9NRP7-1

Frequencies

GnomAD3 genomes

AF:

0.0909

AC:

10439

AN:

114794

Hom.:

1175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.323

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0484

Gnomad ASJ

AF:

0.0163

Gnomad EAS

AF:

0.00302

Gnomad SAS

AF:

0.0112

Gnomad FIN

AF:

0.00483

Gnomad MID

AF:

0.0748

Gnomad NFE

AF:

0.00637

Gnomad OTH

AF:

0.0912

GnomAD3 exomes

AF:

0.202

AC:

11990

AN:

59338

Hom.:

AF XY:

0.193

AC XY:

6032

AN XY:

31242

show subpopulations

Gnomad AFR exome

AF:

0.247

Gnomad AMR exome

AF:

0.277

Gnomad ASJ exome

AF:

0.225

Gnomad EAS exome

AF:

0.223

Gnomad SAS exome

AF:

0.205

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.167

Gnomad OTH exome

AF:

0.244

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.250

AC:

247510

AN:

989400

Hom.:

Cov.:

AF XY:

0.248

AC XY:

121812

AN XY:

490236

show subpopulations

Gnomad4 AFR exome

AF:

0.325

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.237

Gnomad4 EAS exome

AF:

0.229

Gnomad4 SAS exome

AF:

0.231

Gnomad4 FIN exome

AF:

0.206

Gnomad4 NFE exome

AF:

0.252

Gnomad4 OTH exome

AF:

0.252

GnomAD4 genome

AF:

0.0910

AC:

10449

AN:

114796

Hom.:

1176

Cov.:

AF XY:

0.0884

AC XY:

4839

AN XY:

54732

show subpopulations

Gnomad4 AFR

AF:

0.323

Gnomad4 AMR

AF:

0.0483

Gnomad4 ASJ

AF:

0.0163

Gnomad4 EAS

AF:

0.00303

Gnomad4 SAS

AF:

0.0112

Gnomad4 FIN

AF:

0.00483

Gnomad4 NFE

AF:

0.00637

Gnomad4 OTH

AF:

0.0901

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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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