3-52498102-A-G

Variant names:

• chr3-52498102-A-G
• rs13326165
• NM_015136.3:c.78+2611A>G

Variant summary

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

The NM_015136.3(STAB1):​c.78+2611A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,114 control chromosomes in the GnomAD database, including 46,354 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 0.78 (46354 hom., cov: 32)
• Consequence: STAB1 NM_015136.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 70 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 (EAS) allele frequency at 95% confidence interval = 0.953 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.78+2611A>G		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.78+2611A>G		intron	N/A	ENSP00000312946.6
	STAB1	ENST00000481607.1	TSL:1	n.133+2611A>G		intron	N/A
	STAB1	ENST00000479355.1	TSL:2	n.123+2611A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118116 AN: 151996 Hom.: 46311 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.777 AC: 118209 AN: 152114 Hom.: 46354 Cov.: 32 AF XY: 0.783 AC XY: 58211 AN XY: 74366

African (AFR) AF: 0.671 AC: 27840 AN: 41460

American (AMR) AF: 0.815 AC: 12462 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2946 AN: 3472

East Asian (EAS) AF: 0.975 AC: 5049 AN: 5178

South Asian (SAS) AF: 0.878 AC: 4239 AN: 4830

European-Finnish (FIN) AF: 0.823 AC: 8709 AN: 10586

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54391 AN: 67982

Other (OTH) AF: 0.773 AC: 1634 AN: 2114

Alfa AF: 0.800 Hom.: 184579

Bravo AF: 0.772

Asia WGS AF: 0.900 AC: 3124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.84
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs13326165; hg19: chr3-52532118;