rs7926485

Variant names:

• chr11-111665946-G-A
• rs7926485
• NM_015191.3:c.317-22055G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-111665946-G-A
• chr11-111665946-G-C
• chr11-111665946-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015191.3(SIK2):​c.317-22055G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,116 control chromosomes in the GnomAD database, including 31,521 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 0.61 (31521 hom., cov: 33)
• Consequence: SIK2 NM_015191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 8 publications found

Genes affected

SIK2 (HGNC:21680): (salt inducible kinase 2) Enables ATP binding activity; magnesium ion binding activity; and protein serine/threonine kinase activity. Involved in intracellular signal transduction and protein autophosphorylation. Predicted to be located in nucleus. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015191.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIK2	NM_015191.3	MANE Select	c.317-22055G>A		intron	N/A	NP_056006.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIK2	ENST00000304987.4	TSL:1 MANE Select	c.317-22055G>A		intron	N/A	ENSP00000305976.3

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93196 AN: 151998 Hom.: 31497 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.613 AC: 93253 AN: 152116 Hom.: 31521 Cov.: 33 AF XY: 0.620 AC XY: 46083 AN XY: 74384

African (AFR) AF: 0.313 AC: 12987 AN: 41486

American (AMR) AF: 0.707 AC: 10810 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2161 AN: 3468

East Asian (EAS) AF: 0.962 AC: 4996 AN: 5194

South Asian (SAS) AF: 0.802 AC: 3868 AN: 4824

European-Finnish (FIN) AF: 0.737 AC: 7775 AN: 10556

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48486 AN: 67988

Other (OTH) AF: 0.606 AC: 1280 AN: 2112

Alfa AF: 0.670 Hom.: 44636

Bravo AF: 0.600

Asia WGS AF: 0.819 AC: 2848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7926485; hg19: chr11-111536670;