NM_002998.4:c.61-28501A>G

Variant names:

• chr8-96564979-A-G
• rs12156240
• NM_002998.4:c.61-28501A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002998.4(SDC2):​c.61-28501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,446 control chromosomes in the GnomAD database, including 11,165 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 0.34 (11165 hom., cov: 30)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDC2	NM_002998.4	c.61-28501A>G		intron_variant	Intron 1 of 4	ENST00000302190.9	NP_002989.2
SDC2	XM_024447228.2	c.-28+27554A>G		intron_variant	Intron 2 of 5		XP_024302996.1
SDC2	XM_047422076.1	c.-28+27554A>G		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.61-28501A>G		intron_variant	Intron 1 of 4	1	NM_002998.4	ENSP00000307046.4
SDC2	ENST00000522911.5	c.-27-28501A>G		intron_variant	Intron 1 of 4	3		ENSP00000427784.1
SDC2	ENST00000518385.5	c.65-37416A>G		intron_variant	Intron 1 of 3	5		ENSP00000429045.1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51486 AN: 151330 Hom.: 11167 Cov.: 30

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.340 AC: 51479 AN: 151446 Hom.: 11165 Cov.: 30 AF XY: 0.334 AC XY: 24725 AN XY: 73968

African (AFR) AF: 0.103 AC: 4268 AN: 41354

American (AMR) AF: 0.334 AC: 5074 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1398 AN: 3464

East Asian (EAS) AF: 0.0515 AC: 266 AN: 5168

South Asian (SAS) AF: 0.252 AC: 1206 AN: 4792

European-Finnish (FIN) AF: 0.459 AC: 4775 AN: 10400

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33187 AN: 67792

Other (OTH) AF: 0.363 AC: 757 AN: 2086

Alfa AF: 0.273 Hom.: 1954

Bravo AF: 0.326

Asia WGS AF: 0.167 AC: 582 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.73
PhyloP100		0.11
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: rs12156240; hg19: chr8-97577207;