rs1836910

Variant names:

• chr8-96599300-C-T
• rs1836910
• NM_002998.4:c.173-3095C>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.173-3095C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,944 control chromosomes in the GnomAD database, including 3,724 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 0.20 (3724 hom., cov: 29)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002998.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDC2	NM_002998.4	MANE Select	c.173-3095C>T		intron	N/A	NP_002989.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDC2	ENST00000302190.9	TSL:1 MANE Select	c.173-3095C>T		intron	N/A	ENSP00000307046.4
	SDC2	ENST00000519914.5	TSL:2	c.86-3095C>T		intron	N/A	ENSP00000428256.1
	SDC2	ENST00000522911.5	TSL:3	c.86-3095C>T		intron	N/A	ENSP00000427784.1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30838 AN: 151824 Hom.: 3725 Cov.: 29

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.203 AC: 30839 AN: 151944 Hom.: 3724 Cov.: 29 AF XY: 0.208 AC XY: 15441 AN XY: 74242

African (AFR) AF: 0.0664 AC: 2754 AN: 41462

American (AMR) AF: 0.190 AC: 2900 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1711 AN: 5142

South Asian (SAS) AF: 0.360 AC: 1730 AN: 4810

European-Finnish (FIN) AF: 0.285 AC: 3001 AN: 10536

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17171 AN: 67946

Other (OTH) AF: 0.200 AC: 420 AN: 2104

Alfa AF: 0.212 Hom.: 726

Bravo AF: 0.186

Asia WGS AF: 0.300 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.43
PhyloP100		-0.31
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: rs1836910; hg19: chr8-97611528;