NM_002998.4:c.60+6418C>T

Variant names:

• chr8-96500749-C-T
• rs2437772
• NM_002998.4:c.60+6418C>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+6418C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 151,438 control chromosomes in the GnomAD database, including 38,249 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 0.71 (38249 hom., cov: 30)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDC2	NM_002998.4	c.60+6418C>T		intron_variant	Intron 1 of 4	ENST00000302190.9	NP_002989.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDC2	ENST00000302190.9	c.60+6418C>T		intron_variant	Intron 1 of 4	1	NM_002998.4	ENSP00000307046.4

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107218 AN: 151326 Hom.: 38209 Cov.: 30

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.709 AC: 107321 AN: 151438 Hom.: 38249 Cov.: 30 AF XY: 0.712 AC XY: 52635 AN XY: 73916

African (AFR) AF: 0.750 AC: 30914 AN: 41200

American (AMR) AF: 0.737 AC: 11235 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2409 AN: 3466

East Asian (EAS) AF: 0.811 AC: 4173 AN: 5148

South Asian (SAS) AF: 0.796 AC: 3831 AN: 4810

European-Finnish (FIN) AF: 0.682 AC: 7055 AN: 10340

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.668 AC: 45367 AN: 67932

Other (OTH) AF: 0.703 AC: 1480 AN: 2106

Alfa AF: 0.682 Hom.: 50275

Bravo AF: 0.711

Asia WGS AF: 0.767 AC: 2665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.078
DANN	Benign	0.55
PhyloP100		-1.7
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: rs2437772; hg19: chr8-97512977;