3-52521300-G-A

Variant names:

• chr3-52521300-G-A
• rs13081028
• NM_015136.3:c.5909-61G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015136.3(STAB1):​c.5909-61G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 1,604,906 control chromosomes in the GnomAD database, including 247,964 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 0.58 (26294 hom., cov: 31)
  • Exomes 𝑓: 0.55 (221670 hom.)
• Consequence: STAB1 NM_015136.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 24 publications found

Genes affected

STAB1 (HGNC:18628): (stabilin 1) 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, 16 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 endocytose ligands such as low density lipoprotein, Gram-positive and Gram-negative bacteria, and advanced glycosylation end products. Supporting its possible role as a scavenger receptor, the protein rapidly cycles between the plasma membrane and early endosomes. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015136.3. 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
	STAB1	NM_015136.3	MANE Select	c.5909-61G>A		intron	N/A	NP_055951.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAB1	ENST00000321725.10	TSL:1 MANE Select	c.5909-61G>A		intron	N/A	ENSP00000312946.6
	STAB1	ENST00000481626.5	TSL:5	n.1232-61G>A		intron	N/A
	STAB1	ENST00000462741.5	TSL:2	n.-61G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88552 AN: 151792 Hom.: 26257 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.574

GnomAD4 exome AF: 0.549 AC: 797371 AN: 1452994 Hom.: 221670 AF XY: 0.542 AC XY: 391832 AN XY: 722864

African (AFR) AF: 0.672 AC: 22439 AN: 33388

American (AMR) AF: 0.647 AC: 28865 AN: 44580

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 14276 AN: 26036

East Asian (EAS) AF: 0.515 AC: 20398 AN: 39636

South Asian (SAS) AF: 0.345 AC: 29622 AN: 85970

European-Finnish (FIN) AF: 0.553 AC: 28017 AN: 50620

Middle Eastern (MID) AF: 0.525 AC: 2624 AN: 4994

European-Non Finnish (NFE) AF: 0.559 AC: 618752 AN: 1107676

Other (OTH) AF: 0.539 AC: 32378 AN: 60094

GnomAD4 genome AF: 0.584 AC: 88646 AN: 151912 Hom.: 26294 Cov.: 31 AF XY: 0.579 AC XY: 42979 AN XY: 74250

African (AFR) AF: 0.658 AC: 27264 AN: 41432

American (AMR) AF: 0.635 AC: 9692 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1897 AN: 3468

East Asian (EAS) AF: 0.464 AC: 2392 AN: 5152

South Asian (SAS) AF: 0.335 AC: 1613 AN: 4816

European-Finnish (FIN) AF: 0.543 AC: 5750 AN: 10584

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38118 AN: 67876

Other (OTH) AF: 0.579 AC: 1221 AN: 2110

Alfa AF: 0.572 Hom.: 33999

Bravo AF: 0.597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.55
PhyloP100		-1.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs13081028; hg19: chr3-52555316; COSMIC: COSV58737812; COSMIC: COSV58737812;