rs2838302

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The ENST00000270162.8(SIK1):​c.1246-36T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: not found (cov: 0)

Consequence

SIK1
ENST00000270162.8 intron

Scores

2

Clinical Significance

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

Conservation

PhyloP100: 0.0940
Variant links:
Genes affected
SIK1 (HGNC:11142): (salt inducible kinase 1) This gene encodes a serine/threonine protein kinase that contains a ubiquitin-associated (UBA) domain. The encoded protein is a member of the adenosine monophosphate-activated kinase (AMPK) subfamily of kinases that play a role in conserved signal transduction pathways. A mutation in this gene is associated with early infantile epileptic encephalopathy 30. [provided by RefSeq, Nov 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 21-43419273-A-G is Benign according to our data. Variant chr21-43419273-A-G is described in ClinVar as [Benign]. Clinvar id is 1332955.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SIK1NM_173354.5 linkuse as main transcriptc.1246-36T>C intron_variant ENST00000270162.8 NP_775490.2
SIK1XM_011529474.3 linkuse as main transcriptc.1099-36T>C intron_variant XP_011527776.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SIK1ENST00000270162.8 linkuse as main transcriptc.1246-36T>C intron_variant 1 NM_173354.5 ENSP00000270162 P1
SIK1ENST00000644871.1 linkuse as main transcript downstream_gene_variant

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD3 exomes
AF:
0.0999
AC:
20915
AN:
209308
Hom.:
1935
AF XY:
0.0982
AC XY:
11161
AN XY:
113652
show subpopulations
Gnomad AFR exome
AF:
0.448
Gnomad AMR exome
AF:
0.0493
Gnomad ASJ exome
AF:
0.103
Gnomad EAS exome
AF:
0.0253
Gnomad SAS exome
AF:
0.116
Gnomad FIN exome
AF:
0.0630
Gnomad NFE exome
AF:
0.0840
Gnomad OTH exome
AF:
0.0970
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.0909
Hom.:
1146
Asia WGS
AF:
0.0980
AC:
342
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Developmental and epileptic encephalopathy, 30 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 15, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.1
DANN
Benign
0.32

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.

Other links and lift over

dbSNP: rs2838302; hg19: chr21-44839153; COSMIC: COSV54259509; COSMIC: COSV54259509; API