rs12453316
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001144952.2(SDK2):c.65-12323G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,214 control chromosomes in the GnomAD database, including 6,561 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 0.26 ( 6561 hom., cov: 33)
Exomes 𝑓: 0.38 ( 0 hom. )
Consequence
SDK2
NM_001144952.2 intron
NM_001144952.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.28
Genes affected
SDK2 (HGNC:19308): (sidekick cell adhesion molecule 2) The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains two immunoglobulin domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. This protein, and a homologous mouse sequence, are very similar to the Drosophila sidekick gene product but the specific function of this superfamily member is not yet known. Evidence for alternative splicing at this gene locus has been observed but the full-length nature of additional variants has not yet been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDK2 | NM_001144952.2 | c.65-12323G>A | intron_variant | ENST00000392650.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDK2 | ENST00000392650.8 | c.65-12323G>A | intron_variant | 5 | NM_001144952.2 | P1 | |||
ENST00000583712.2 | n.2828C>T | non_coding_transcript_exon_variant | 3/3 | 5 | |||||
ENST00000655723.1 | n.1137C>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.265 AC: 40242AN: 152084Hom.: 6560 Cov.: 33
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GnomAD4 exome AF: 0.375 AC: 3AN: 8Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1AN XY: 4
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GnomAD4 genome ? AF: 0.264 AC: 40248AN: 152206Hom.: 6561 Cov.: 33 AF XY: 0.266 AC XY: 19766AN XY: 74410
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at