Variant chr11-116861796-G-T 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_001366686.3(SIK3):c.2315+45C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 1,310,282 control chromosomes in the GnomAD database, including 480,150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.85 ( 56248 hom., cov: 32)

Exomes 𝑓: 0.85 ( 423902 hom. )

Consequence

SIK3
NM_001366686.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.575

Variant links:

Genes affected

SIK3 (HGNC:29165): (SIK family kinase 3) Enables ATP binding activity; magnesium ion binding activity; and protein serine/threonine kinase activity. Involved in positive regulation of TORC1 signaling; positive regulation of TORC2 signaling; and protein phosphorylation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SIK3 links:

SIK3 (HGNC:):

SIK3 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=-0.91).

BP6

Variant 11-116861796-G-T is Benign according to our data. Variant chr11-116861796-G-T is described in ClinVar as [Benign]. Clinvar id is 1332965.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIK3	NM_001366686.3 linkuse as main transcript	c.2315+45C>A		intron_variant		ENST00000445177.6	NP_001353615.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIK3	ENST00000445177.6 linkuse as main transcript	c.2315+45C>A		intron_variant		5	NM_001366686.3	ENSP00000391295.2		H0Y4E8

Frequencies

GnomAD3 genomes

AF:

0.854

AC:

129887

AN:

152024

Hom.:

56211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.918

Gnomad AMI

AF:

0.971

Gnomad AMR

AF:

0.757

Gnomad ASJ

AF:

0.826

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.671

Gnomad FIN

AF:

0.812

Gnomad MID

AF:

0.804

Gnomad NFE

AF:

0.886

Gnomad OTH

AF:

0.842

GnomAD3 exomes

AF:

0.798

AC:

175287

AN:

219536

Hom.:

71596

AF XY:

0.798

AC XY:

93737

AN XY:

117518

show subpopulations

Gnomad AFR exome

AF:

0.916

Gnomad AMR exome

AF:

0.704

Gnomad ASJ exome

AF:

0.826

Gnomad EAS exome

AF:

0.488

Gnomad SAS exome

AF:

0.688

Gnomad FIN exome

AF:

0.824

Gnomad NFE exome

AF:

0.885

Gnomad OTH exome

AF:

0.820

GnomAD4 exome

AF:

0.850

AC:

984460

AN:

1158140

Hom.:

423902

Cov.:

AF XY:

0.845

AC XY:

495982

AN XY:

587218

show subpopulations

Gnomad4 AFR exome

AF:

0.915

Gnomad4 AMR exome

AF:

0.714

Gnomad4 ASJ exome

AF:

0.825

Gnomad4 EAS exome

AF:

0.475

Gnomad4 SAS exome

AF:

0.686

Gnomad4 FIN exome

AF:

0.824

Gnomad4 NFE exome

AF:

0.890

Gnomad4 OTH exome

AF:

0.835

GnomAD4 genome

AF:

0.854

AC:

129971

AN:

152142

Hom.:

56248

Cov.:

AF XY:

0.844

AC XY:

62767

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.918

Gnomad4 AMR

AF:

0.756

Gnomad4 ASJ

AF:

0.826

Gnomad4 EAS

AF:

0.481

Gnomad4 SAS

AF:

0.671

Gnomad4 FIN

AF:

0.812

Gnomad4 NFE

AF:

0.886

Gnomad4 OTH

AF:

0.833

Alfa

AF:

0.866

Hom.:

100486

Bravo

AF:

0.856

Asia WGS

AF:

0.598

AC:

2082

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Spondyloepimetaphyseal dysplasia, Krakow type

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.15

DANN

Benign

0.40

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