rs2582846

Positions:

• chr8-96561454-T-A
• chr8-96561454-T-G

Variant summary

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

The NM_002998.4(SDC2):​c.61-32026T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,060 control chromosomes in the GnomAD database, including 33,680 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 0.63 (33680 hom., cov: 31)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

Genes affected

SDC2 (HGNC:10659): (syndecan 2) The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-2 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-2 expression has been detected in several different tumor types. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDC2	NM_002998.4	c.61-32026T>A		intron_variant		ENST00000302190.9	NP_002989.2
SDC2	XM_024447228.2	c.-28+24029T>A		intron_variant			XP_024302996.1
SDC2	XM_047422076.1	c.-28+24029T>A		intron_variant			XP_047278032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDC2	ENST00000302190.9	c.61-32026T>A		intron_variant		1	NM_002998.4	ENSP00000307046	P1
SDC2	ENST00000518385.5	c.65-40941T>A		intron_variant		5		ENSP00000429045
SDC2	ENST00000522911.5	c.-27-32026T>A		intron_variant		3		ENSP00000427784

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95756 AN: 151942 Hom.: 33692 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.630 AC: 95747 AN: 152060 Hom.: 33680 Cov.: 31 AF XY: 0.626 AC XY: 46542 AN XY: 74334

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.645

Alfa AF: 0.692 Hom.: 4283

Bravo AF: 0.600

Asia WGS AF: 0.567 AC: 1974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
DANN	Benign	0.65

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: rs2582846; hg19: chr8-97573682;