8-96552433-C-A

Position:

• chr8-96552433-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_002998.4(SDC2):​c.61-41047C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,972 control chromosomes in the GnomAD database, including 21,592 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 0.50 (21592 hom., cov: 32)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDC2	NM_002998.4	c.61-41047C>A		intron_variant		ENST00000302190.9
LOC124900253	XR_007061018.1	n.12594C>A		non_coding_transcript_exon_variant	2/2
SDC2	XM_024447228.2	c.-28+15008C>A		intron_variant
SDC2	XM_047422076.1	c.-28+15008C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDC2	ENST00000302190.9	c.61-41047C>A		intron_variant		1	NM_002998.4	P1
SDC2	ENST00000518385.5	c.65-49962C>A		intron_variant		5
SDC2	ENST00000522911.5	c.-27-41047C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75989 AN: 151854 Hom.: 21595 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.500 AC: 75993 AN: 151972 Hom.: 21592 Cov.: 32 AF XY: 0.494 AC XY: 36671 AN XY: 74274

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.539

Alfa AF: 0.617 Hom.: 29104

Bravo AF: 0.480

Asia WGS AF: 0.390 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	14
DANN	Benign	0.88

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

Publications

LitVar

Other links and lift over

dbSNP: rs1444573; hg19: chr8-97564661;