rs1582881

Positions:

• chr12-103594117-A-G
• chr12-103594117-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017564.10(STAB2):​c.216-278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,080 control chromosomes in the GnomAD database, including 27,779 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 0.59 (27779 hom., cov: 32)
• Consequence: STAB2 NM_017564.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

STAB2 (HGNC:18629): (stabilin 2) This gene encodes a large, transmembrane receptor protein which may function in angiogenesis, lymphocyte homing, cell adhesion, or receptor scavenging. The protein contains 7 fasciclin, 15 epidermal growth factor (EGF)-like, and 2 laminin-type EGF-like domains as well as a C-type lectin-like hyaluronan-binding Link module. The protein is primarily expressed on sinusoidal endothelial cells of liver, spleen, and lymph node. The receptor has been shown to bind and endocytose ligands such as hyaluronan, low density lipoprotein, Gram-positive and Gram-negative bacteria, and advanced glycosylation end products. Supporting its possible role as a scavenger receptor, the protein has been shown to cycle between the plasma membrane and lysosomes. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAB2	NM_017564.10	c.216-278A>G		intron_variant		ENST00000388887.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAB2	ENST00000388887.7	c.216-278A>G		intron_variant		1	NM_017564.10	P1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89007 AN: 151962 Hom.: 27725 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.586 AC: 89120 AN: 152080 Hom.: 27779 Cov.: 32 AF XY: 0.582 AC XY: 43269 AN XY: 74358

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.566

Alfa AF: 0.518 Hom.: 42215

Bravo AF: 0.590

Asia WGS AF: 0.547 AC: 1905 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.51

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: rs1582881; hg19: chr12-103987895;