rs2651472

Variant names:

• chr8-96584445-G-A
• NM_002998.4:c.61-9035G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-96584445-G-A
• chr8-96584445-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002998.4(SDC2):​c.61-9035G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: SDC2 NM_002998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDC2	NM_002998.4	c.61-9035G>A		intron_variant	Intron 1 of 4	ENST00000302190.9	NP_002989.2
SDC2	XM_011517212.4	c.-184+176G>A		intron_variant	Intron 1 of 5		XP_011515514.1
SDC2	XM_024447228.2	c.-27-9035G>A		intron_variant	Intron 2 of 5		XP_024302996.1
SDC2	XM_047422076.1	c.-27-9035G>A		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.61-9035G>A		intron_variant	Intron 1 of 4	1	NM_002998.4	ENSP00000307046.4
SDC2	ENST00000519914.5	c.-28+3877G>A		intron_variant	Intron 1 of 4	2		ENSP00000428256.1
SDC2	ENST00000522911.5	c.-27-9035G>A		intron_variant	Intron 1 of 4	3		ENSP00000427784.1
SDC2	ENST00000518385.5	c.65-17950G>A		intron_variant	Intron 1 of 3	5		ENSP00000429045.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.9
DANN	Benign	0.79

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-97596673;