rs2439525

Variant names:

• chr8-96524813-C-T
• rs2439525
• NM_002998.4:c.60+30482C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.88).
• 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 rank	MANE	Protein	UniProt
SDC2	NM_002998.4	c.60+30482C>T		intron_variant	Intron 1 of 4	ENST00000302190.9	NP_002989.2
SDC2	XM_024447228.2	c.-4612C>T		5_prime_UTR_variant	Exon 1 of 6		XP_024302996.1
SDC2	XM_047422076.1	c.-12640C>T		5_prime_UTR_variant	Exon 1 of 5		XP_047278032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDC2	ENST00000302190.9	c.60+30482C>T		intron_variant	Intron 1 of 4	1	NM_002998.4	ENSP00000307046.4

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

African (AFR) AF: 0.822 AC: 34132 AN: 41504

American (AMR) AF: 0.644 AC: 9839 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2840 AN: 3472

East Asian (EAS) AF: 0.420 AC: 2172 AN: 5168

South Asian (SAS) AF: 0.642 AC: 3099 AN: 4826

European-Finnish (FIN) AF: 0.756 AC: 7991 AN: 10574

Middle Eastern (MID) AF: 0.846 AC: 247 AN: 292

European-Non Finnish (NFE) AF: 0.810 AC: 55072 AN: 68002

Other (OTH) AF: 0.778 AC: 1641 AN: 2108

Alfa AF: 0.804 Hom.: 65575

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
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2439525; hg19: chr8-97537041;