rs2439525

chr8-96524813-C-T

Variant summary

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

The NM_002998.4(SDC2):c.60+30482C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,146 control chromosomes in the GnomAD database, including 46,404 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 0.77 (46404 hom., cov: 32)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDC2	NM_002998.4	c.60+30482C>T		intron_variant		ENST00000302190.9
SDC2	XM_024447228.2	c.-4612C>T		5_prime_UTR_variant	1/6
SDC2	XM_047422076.1	c.-12640C>T		5_prime_UTR_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDC2	ENST00000302190.9	c.60+30482C>T		intron_variant		1	NM_002998.4	P1

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117662 AN: 152028 Hom.: 46359 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.774 AC: 117759 AN: 152146 Hom.: 46404 Cov.: 32 AF XY: 0.763 AC XY: 56749 AN XY: 74372

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.778

Alfa AF: 0.803 Hom.: 56845

Bravo AF: 0.772

Asia WGS AF: 0.561 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.8
Dann	Benign	0.50

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: rs2439525; hg19: chr8-97537041;