Variant chr2-218675543-A-G 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.434+70A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 1,091,832 control chromosomes in the GnomAD database, including 1,480 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.090 ( 802 hom., cov: 21)

Exomes 𝑓: 0.0073 ( 678 hom. )

Consequence

STK36
NM_015690.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.40

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 2-218675543-A-G is Benign according to our data. Variant chr2-218675543-A-G is described in ClinVar as [Benign]. Clinvar id is 1231128.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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+70A>G		intron_variant		ENST00000295709.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
STK36	ENST00000295709.8 linkuse as main transcript	c.434+70A>G	intron_variant	1	NM_015690.5	P1	Q9NRP7-1
STK36	ENST00000392105.7 linkuse as main transcript	c.434+70A>G	intron_variant	1			Q9NRP7-2
STK36	ENST00000424080.1 linkuse as main transcript	c.434+70A>G	intron_variant	5
STK36	ENST00000440309.5 linkuse as main transcript	c.434+70A>G	intron_variant	5		P1	Q9NRP7-1

Frequencies

GnomAD3 genomes

AF:

0.0901

AC:

8112

AN:

90016

Hom.:

802

Cov.:

show subpopulations

Gnomad AFR

AF:

0.292

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0464

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00114

Gnomad FIN

AF:

0.000752

Gnomad MID

AF:

0.0439

Gnomad NFE

AF:

0.00127

Gnomad OTH

AF:

0.0724

GnomAD4 exome

AF:

0.00731

AC:

7320

AN:

1001776

Hom.:

678

AF XY:

0.00628

AC XY:

3184

AN XY:

506908

show subpopulations

Gnomad4 AFR exome

AF:

0.233

Gnomad4 AMR exome

AF:

0.0108

Gnomad4 ASJ exome

AF:

0.0000543

Gnomad4 EAS exome

AF:

0.0000320

Gnomad4 SAS exome

AF:

0.000833

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000464

Gnomad4 OTH exome

AF:

0.0163

GnomAD4 genome

AF:

0.0901

AC:

8115

AN:

90056

Hom.:

802

Cov.:

AF XY:

0.0937

AC XY:

3905

AN XY:

41692

show subpopulations

Gnomad4 AFR

AF:

0.291

Gnomad4 AMR

AF:

0.0462

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00114

Gnomad4 FIN

AF:

0.000752

Gnomad4 NFE

AF:

0.00127

Gnomad4 OTH

AF:

0.0711

Alfa

AF:

0.000372

Hom.:

Bravo

AF:

0.0681

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

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.9

DANN

Benign

0.34

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