Variant chr3-52521941-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_015136.3(STAB1):c.6261T>C(p.Arg2087Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 1,607,774 control chromosomes in the GnomAD database, including 254,042 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 0.60 ( 27979 hom., cov: 34)

Exomes 𝑓: 0.55 ( 226063 hom. )

Consequence

STAB1
NM_015136.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.58

Variant links:

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]

STAB1 links:

STAB1 (HGNC:):

STAB1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-2.58 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAB1	NM_015136.3 linkuse as main transcript	c.6261T>C	p.Arg2087Arg	synonymous_variant	58/69	ENST00000321725.10	NP_055951.2	Q9NY15-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
STAB1	ENST00000321725.10 linkuse as main transcript	c.6261T>C	p.Arg2087Arg	synonymous_variant	58/69	1	NM_015136.3	ENSP00000312946.6	Q9NY15-1
STAB1	ENST00000462681.1 linkuse as main transcript	n.374T>C		non_coding_transcript_exon_variant	1/4	1
STAB1	ENST00000462741.5 linkuse as main transcript	n.496T>C		non_coding_transcript_exon_variant	2/12	2
STAB1	ENST00000481626.5 linkuse as main transcript	n.1584T>C		non_coding_transcript_exon_variant	8/15	5

Frequencies

GnomAD3 genomes

AF:

0.600

AC:

91159

AN:

151986

Hom.:

27944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.706

Gnomad AMI

AF:

0.576

Gnomad AMR

AF:

0.644

Gnomad ASJ

AF:

0.554

Gnomad EAS

AF:

0.468

Gnomad SAS

AF:

0.345

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.565

Gnomad OTH

AF:

0.586

GnomAD3 exomes

AF:

0.552

AC:

136175

AN:

246672

Hom.:

38788

AF XY:

0.538

AC XY:

71842

AN XY:

133642

show subpopulations

Gnomad AFR exome

AF:

0.712

Gnomad AMR exome

AF:

0.657

Gnomad ASJ exome

AF:

0.549

Gnomad EAS exome

AF:

0.452

Gnomad SAS exome

AF:

0.349

Gnomad FIN exome

AF:

0.558

Gnomad NFE exome

AF:

0.567

Gnomad OTH exome

AF:

0.545

GnomAD4 exome

AF:

0.554

AC:

805857

AN:

1455670

Hom.:

226063

Cov.:

AF XY:

0.547

AC XY:

395437

AN XY:

723240

show subpopulations

Gnomad4 AFR exome

AF:

0.720

Gnomad4 AMR exome

AF:

0.652

Gnomad4 ASJ exome

AF:

0.557

Gnomad4 EAS exome

AF:

0.524

Gnomad4 SAS exome

AF:

0.354

Gnomad4 FIN exome

AF:

0.554

Gnomad4 NFE exome

AF:

0.562

Gnomad4 OTH exome

AF:

0.545

GnomAD4 genome

AF:

0.600

AC:

91247

AN:

152104

Hom.:

27979

Cov.:

AF XY:

0.595

AC XY:

44251

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.706

Gnomad4 AMR

AF:

0.644

Gnomad4 ASJ

AF:

0.554

Gnomad4 EAS

AF:

0.467

Gnomad4 SAS

AF:

0.346

Gnomad4 FIN

AF:

0.544

Gnomad4 NFE

AF:

0.565

Gnomad4 OTH

AF:

0.591

Alfa

AF:

0.569

Hom.:

26898

Bravo

AF:

0.615

Asia WGS

AF:

0.463

AC:

1613

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.50

DANN

Benign

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over