chr8-96539550-G-C

Variant names:

• chr8-96539550-G-C
• rs2582831
• NM_002998.4:c.60+45219G>C

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+45219G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,082 control chromosomes in the GnomAD database, including 26,674 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 0.57 (26674 hom., cov: 33)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 1 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]

LOC124900253 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDC2	NM_002998.4	c.60+45219G>C		intron_variant	Intron 1 of 4	ENST00000302190.9	NP_002989.2
LOC124900253	XR_007061018.1	n.1364G>C		non_coding_transcript_exon_variant	Exon 1 of 2
SDC2	XM_024447228.2	c.-28+2125G>C		intron_variant	Intron 2 of 5		XP_024302996.1
SDC2	XM_047422076.1	c.-28+2125G>C		intron_variant	Intron 1 of 4		XP_047278032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDC2	ENST00000302190.9	c.60+45219G>C		intron_variant	Intron 1 of 4	1	NM_002998.4	ENSP00000307046.4
SDC2	ENST00000522911.5	c.-28+45507G>C		intron_variant	Intron 1 of 4	3		ENSP00000427784.1
SDC2	ENST00000518385.5	c.64+45215G>C		intron_variant	Intron 1 of 3	5		ENSP00000429045.1

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87228 AN: 151964 Hom.: 26669 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.574 AC: 87256 AN: 152082 Hom.: 26674 Cov.: 33 AF XY: 0.567 AC XY: 42170 AN XY: 74334

African (AFR) AF: 0.375 AC: 15545 AN: 41458

American (AMR) AF: 0.543 AC: 8305 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2172 AN: 5158

South Asian (SAS) AF: 0.443 AC: 2135 AN: 4818

European-Finnish (FIN) AF: 0.656 AC: 6934 AN: 10576

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47713 AN: 68000

Other (OTH) AF: 0.608 AC: 1286 AN: 2114

Alfa AF: 0.628 Hom.: 3851

Bravo AF: 0.558

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.79
DANN	Benign	0.52
PhyloP100		-0.70
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: rs2582831; hg19: chr8-97551778;