8-96493168-G-C

Variant names:

• chr8-96493168-G-C
• rs2452993
• ENST00000932834.1:c.-705G>C

Variant summary

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

The ENST00000932834.1(SDC2):​c.-705G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,998 control chromosomes in the GnomAD database, including 17,342 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 0.47 (17342 hom., cov: 33)
• Consequence: SDC2 ENST00000932834.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000932834.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDC2	ENST00000932834.1		c.-705G>C		upstream_gene	N/A	ENSP00000602893.1

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71474 AN: 151880 Hom.: 17307 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.471 AC: 71572 AN: 151998 Hom.: 17342 Cov.: 33 AF XY: 0.474 AC XY: 35180 AN XY: 74296

African (AFR) AF: 0.569 AC: 23564 AN: 41440

American (AMR) AF: 0.555 AC: 8482 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2684 AN: 5164

South Asian (SAS) AF: 0.494 AC: 2376 AN: 4810

European-Finnish (FIN) AF: 0.433 AC: 4566 AN: 10544

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26490 AN: 67966

Other (OTH) AF: 0.462 AC: 974 AN: 2110

Alfa AF: 0.429 Hom.: 1830

Bravo AF: 0.487

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.48
PhyloP100		0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2452993; hg19: chr8-97505396;