rs13081028

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-52521300-G-A
• chr3-52521300-G-C
• chr3-52521300-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAB1	NM_015136.3	c.5909-61G>A		intron_variant	Intron 55 of 68	ENST00000321725.10	NP_055951.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAB1	ENST00000321725.10	c.5909-61G>A		intron_variant	Intron 55 of 68	1	NM_015136.3	ENSP00000312946.6
STAB1	ENST00000481626.5	n.1232-61G>A		intron_variant	Intron 5 of 14	5
STAB1	ENST00000462741.5	n.-61G>A		upstream_gene_variant		2

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

Gnomad4 AFR exome AF: 0.672

Gnomad4 AMR exome AF: 0.647

Gnomad4 ASJ exome AF: 0.548

Gnomad4 EAS exome AF: 0.515

Gnomad4 SAS exome AF: 0.345

Gnomad4 FIN exome AF: 0.553

Gnomad4 NFE exome AF: 0.559

Gnomad4 OTH exome AF: 0.539

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

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.579

Alfa AF: 0.561 Hom.: 21875

Bravo AF: 0.597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.55
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs13081028; hg19: chr3-52555316; COSMIC: COSV58737812; COSMIC: COSV58737812;