rs2651472

chr8-96584445-G-T

Variant summary

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

The NM_002998.4(SDC2):c.61-9035G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,160 control chromosomes in the GnomAD database, including 13,569 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 0.39 (13569 hom., cov: 33)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

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=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDC2	NM_002998.4	c.61-9035G>T		intron_variant		ENST00000302190.9
SDC2	XM_011517212.4	c.-184+176G>T		intron_variant
SDC2	XM_024447228.2	c.-27-9035G>T		intron_variant
SDC2	XM_047422076.1	c.-27-9035G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDC2	ENST00000302190.9	c.61-9035G>T		intron_variant		1	NM_002998.4	P1
SDC2	ENST00000518385.5	c.65-17950G>T		intron_variant		5
SDC2	ENST00000519914.5	c.-28+3877G>T		intron_variant		2
SDC2	ENST00000522911.5	c.-27-9035G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59896 AN: 152042 Hom.: 13573 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.394 AC: 59894 AN: 152160 Hom.: 13569 Cov.: 33 AF XY: 0.390 AC XY: 28972 AN XY: 74368

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.429

Alfa AF: 0.471 Hom.: 3590

Bravo AF: 0.387

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	8.1
Dann	Benign	0.75

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: rs2651472; hg19: chr8-97596673;