rs1010554

Variant names:

• chr3-52508903-T-C
• rs1010554
• NM_015136.3:c.2236-307T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-52508903-T-C
• chr3-52508903-T-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.2236-307T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,984 control chromosomes in the GnomAD database, including 23,458 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 0.54 (23458 hom., cov: 32)
• Consequence: STAB1 NM_015136.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 18 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.72 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.2236-307T>C		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.2236-307T>C		intron	N/A	ENSP00000312946.6
	STAB1	ENST00000484850.1	TSL:3	n.154-307T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82252 AN: 151870 Hom.: 23435 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.542 AC: 82328 AN: 151984 Hom.: 23458 Cov.: 32 AF XY: 0.543 AC XY: 40344 AN XY: 74284

African (AFR) AF: 0.710 AC: 29396 AN: 41432

American (AMR) AF: 0.429 AC: 6546 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3470

East Asian (EAS) AF: 0.542 AC: 2805 AN: 5176

South Asian (SAS) AF: 0.741 AC: 3565 AN: 4814

European-Finnish (FIN) AF: 0.468 AC: 4924 AN: 10528

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31741 AN: 67970

Other (OTH) AF: 0.518 AC: 1093 AN: 2112

Alfa AF: 0.494 Hom.: 34786

Bravo AF: 0.544

Asia WGS AF: 0.605 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.3
DANN	Benign	0.65
PhyloP100		-0.63
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: rs1010554; hg19: chr3-52542919;