rs2000615

Positions:

• chr11-117045103-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366686.3(SIK3):​c.273+53040G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,160 control chromosomes in the GnomAD database, including 56,435 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.86 (56435 hom., cov: 31)
• Consequence: SIK3 NM_001366686.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIK3	NM_001366686.3	c.273+53040G>A		intron_variant		ENST00000445177.6	NP_001353615.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIK3	ENST00000445177.6	c.273+53040G>A		intron_variant		5	NM_001366686.3	ENSP00000391295	A2

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130192 AN: 152042 Hom.: 56397 Cov.: 31

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.847

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.856 AC: 130275 AN: 152160 Hom.: 56435 Cov.: 31 AF XY: 0.847 AC XY: 63020 AN XY: 74372

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.839

Alfa AF: 0.875 Hom.: 8279

Bravo AF: 0.860

Asia WGS AF: 0.602 AC: 2096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.38
DANN	Benign	0.31
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs2000615; hg19: chr11-116915819;