12-103594117-A-G

Variant names:

• chr12-103594117-A-G
• rs1582881
• NM_017564.10:c.216-278A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017564.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAB2	NM_017564.10	MANE Select	c.216-278A>G		intron	N/A	NP_060034.9

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAB2	ENST00000388887.7	TSL:1 MANE Select	c.216-278A>G		intron	N/A	ENSP00000373539.2

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

African (AFR) AF: 0.817 AC: 33890 AN: 41498

American (AMR) AF: 0.489 AC: 7469 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1621 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1971 AN: 5178

South Asian (SAS) AF: 0.541 AC: 2606 AN: 4820

European-Finnish (FIN) AF: 0.516 AC: 5457 AN: 10568

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34451 AN: 67960

Other (OTH) AF: 0.566 AC: 1195 AN: 2112

Alfa AF: 0.528 Hom.: 93183

Bravo AF: 0.590

Asia WGS AF: 0.547 AC: 1905 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-0.027
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: rs1582881; hg19: chr12-103987895;