3-52495757-T-G

Variant names:

• chr3-52495757-T-G
• rs9846089
• NM_015136.3:c.78+266T>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+266T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.963 in 152,314 control chromosomes in the GnomAD database, including 70,656 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 0.96 (70656 hom., cov: 35)
• Consequence: STAB1 NM_015136.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAB1	NM_015136.3	c.78+266T>G		intron_variant	Intron 1 of 68	ENST00000321725.10	NP_055951.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAB1	ENST00000321725.10	c.78+266T>G		intron_variant	Intron 1 of 68	1	NM_015136.3	ENSP00000312946.6
STAB1	ENST00000481607.1	n.133+266T>G		intron_variant	Intron 1 of 20	1
STAB1	ENST00000479355.1	n.123+266T>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.963 AC: 146539 AN: 152196 Hom.: 70596 Cov.: 35

Gnomad AFR AF: 0.990

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.957

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

GnomAD4 genome AF: 0.963 AC: 146658 AN: 152314 Hom.: 70656 Cov.: 35 AF XY: 0.965 AC XY: 71859 AN XY: 74476

African (AFR) AF: 0.990 AC: 41148 AN: 41570

American (AMR) AF: 0.948 AC: 14512 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 3368 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5076 AN: 5184

South Asian (SAS) AF: 0.980 AC: 4729 AN: 4826

European-Finnish (FIN) AF: 0.969 AC: 10302 AN: 10630

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64376 AN: 68008

Other (OTH) AF: 0.956 AC: 2020 AN: 2112

Alfa AF: 0.960 Hom.: 8715

Bravo AF: 0.962

Asia WGS AF: 0.965 AC: 3358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.4
DANN	Benign	0.64
PhyloP100		-0.33
PromoterAI		-0.021	Neutral
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: rs9846089; hg19: chr3-52529773;