chr11-116851110-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001366686.3(SIK3):​c.3656-1827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,216 control chromosomes in the GnomAD database, including 48,214 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 0.79 ( 48214 hom., cov: 34)

Consequence

SIK3
NM_001366686.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.824
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]
APOA1-AS (HGNC:40079): (APOA1 antisense RNA)

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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=-0.99).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SIK3NM_001366686.3 linkuse as main transcriptc.3656-1827G>A intron_variant ENST00000445177.6 NP_001353615.1
APOA1-ASNR_126362.1 linkuse as main transcriptn.124-4180C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SIK3ENST00000445177.6 linkuse as main transcriptc.3656-1827G>A intron_variant 5 NM_001366686.3 ENSP00000391295 A2
APOA1-ASENST00000669664.1 linkuse as main transcriptn.75-2760C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.790
AC:
120198
AN:
152098
Hom.:
48164
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.812
Gnomad AMI
AF:
0.943
Gnomad AMR
AF:
0.736
Gnomad ASJ
AF:
0.781
Gnomad EAS
AF:
0.403
Gnomad SAS
AF:
0.588
Gnomad FIN
AF:
0.753
Gnomad MID
AF:
0.706
Gnomad NFE
AF:
0.838
Gnomad OTH
AF:
0.800
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.790
AC:
120293
AN:
152216
Hom.:
48214
Cov.:
34
AF XY:
0.781
AC XY:
58139
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.812
Gnomad4 AMR
AF:
0.735
Gnomad4 ASJ
AF:
0.781
Gnomad4 EAS
AF:
0.404
Gnomad4 SAS
AF:
0.590
Gnomad4 FIN
AF:
0.753
Gnomad4 NFE
AF:
0.838
Gnomad4 OTH
AF:
0.793
Alfa
AF:
0.820
Hom.:
103874
Bravo
AF:
0.792
Asia WGS
AF:
0.512
AC:
1783
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.21
DANN
Benign
0.55

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: rs10047459; hg19: chr11-116721826; API