rs12453316

chr17-73519920-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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
• 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]

(HGNC:):

ACMG classification

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: 40242 AN: 152084 Hom.: 6560 Cov.: 33

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.287

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.264 AC: 40248 AN: 152206 Hom.: 6561 Cov.: 33 AF XY: 0.266 AC XY: 19766 AN XY: 74410

Gnomad4 AFR AF: 0.0698

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.287

Alfa AF: 0.342 Hom.: 5136

Bravo AF: 0.246

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	20
Dann	Benign	0.91

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: rs12453316; hg19: chr17-71516059;