rs2437780

Variant names:

• chr8-96507448-T-A
• rs2437780
• NM_002998.4:c.60+13117T>A

Your query was ambiguous. Multiple possible variants found:

• chr8-96507448-T-A
• chr8-96507448-T-C
• chr8-96507448-T-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.60+13117T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,078 control chromosomes in the GnomAD database, including 38,552 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 (38552 hom., cov: 33)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDC2	NM_002998.4	c.60+13117T>A		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+13117T>A		intron_variant	Intron 1 of 4	1	NM_002998.4	ENSP00000307046.4

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107846 AN: 151960 Hom.: 38513 Cov.: 33

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.710 AC: 107948 AN: 152078 Hom.: 38552 Cov.: 33 AF XY: 0.713 AC XY: 52986 AN XY: 74326

African (AFR) AF: 0.756 AC: 31372 AN: 41480

American (AMR) AF: 0.738 AC: 11275 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2408 AN: 3468

East Asian (EAS) AF: 0.811 AC: 4195 AN: 5170

South Asian (SAS) AF: 0.785 AC: 3788 AN: 4824

European-Finnish (FIN) AF: 0.680 AC: 7194 AN: 10574

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45371 AN: 67964

Other (OTH) AF: 0.704 AC: 1486 AN: 2110

Alfa AF: 0.690 Hom.: 4272

Bravo AF: 0.713

Asia WGS AF: 0.760 AC: 2639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.67
PhyloP100		0.30
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: rs2437780; hg19: chr8-97519676;