dbSNP rs1609860: STAB2:p.Pro510His (chr12-103654676-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017564.10(STAB2):c.1529C>A(p.Pro510His) variant causes a missense change. The variant allele was found at a frequency of 0.0903 in 1,613,778 control chromosomes in the GnomAD database, including 7,556 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P510R) has been classified as Benign.

Frequency

Genomes: 𝑓 0.078 ( 636 hom., cov: 32)

Exomes 𝑓: 0.092 ( 6920 hom. )

Consequence

STAB2
NM_017564.10 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.41

Publications

26 publications found

Variant links:

Genes affected

STAB2 (HGNC:18629): (stabilin 2) 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, 15 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 bind and endocytose ligands such as hyaluronan, low density lipoprotein, Gram-positive and Gram-negative bacteria, and advanced glycosylation end products. Supporting its possible role as a scavenger receptor, the protein has been shown to cycle between the plasma membrane and lysosomes. [provided by RefSeq, Jul 2008]

STAB2 links:

ENSG00000257737 (HGNC:):

ENSG00000257737 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0023873448).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAB2	NM_017564.10 link	c.1529C>A	p.Pro510His	missense_variant	Exon 13 of 69	ENST00000388887.7	NP_060034.9	Q8WWQ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAB2	ENST00000388887.7 link	c.1529C>A	p.Pro510His	missense_variant	Exon 13 of 69	1	NM_017564.10	ENSP00000373539.2		Q8WWQ8
ENSG00000257737	ENST00000551905.1 link	n.*104G>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0781

AC:

11884

AN:

152124

Hom.:

634

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0151

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.0804

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.184

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0858

Gnomad OTH

AF:

0.0946

GnomAD2 exomes

AF:

0.102

AC:

25516

AN:

251072

AF XY:

0.106

show subpopulations

Gnomad AFR exome

AF:

0.0134

Gnomad AMR exome

AF:

0.104

Gnomad ASJ exome

AF:

0.0806

Gnomad EAS exome

AF:

0.106

Gnomad FIN exome

AF:

0.175

Gnomad NFE exome

AF:

0.0852

Gnomad OTH exome

AF:

0.101

GnomAD4 exome

AF:

0.0916

AC:

133862

AN:

1461536

Hom.:

6920

Cov.:

AF XY:

0.0943

AC XY:

68575

AN XY:

727054

show subpopulations

African (AFR)

AF:

0.0127

AC:

425

AN:

33464

American (AMR)

AF:

0.102

AC:

4552

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.0807

AC:

2107

AN:

26118

East Asian (EAS)

AF:

0.138

AC:

5459

AN:

39690

South Asian (SAS)

AF:

0.163

AC:

14030

AN:

86174

European-Finnish (FIN)

AF:

0.171

AC:

9129

AN:

53416

Middle Eastern (MID)

AF:

0.121

AC:

696

AN:

5768

European-Non Finnish (NFE)

AF:

0.0822

AC:

91346

AN:

1111864

Other (OTH)

AF:

0.101

AC:

6118

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

5937

11874

17811

23748

29685

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0781

AC:

11884

AN:

152242

Hom.:

636

Cov.:

AF XY:

0.0848

AC XY:

6316

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.0151

AC:

626

AN:

41544

American (AMR)

AF:

0.103

AC:

1573

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0804

AC:

279

AN:

3470

East Asian (EAS)

AF:

0.114

AC:

593

AN:

5182

South Asian (SAS)

AF:

0.160

AC:

772

AN:

4820

European-Finnish (FIN)

AF:

0.184

AC:

1951

AN:

10600

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0858

AC:

5838

AN:

68022

Other (OTH)

AF:

0.0979

AC:

207

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

552

1104

1656

2208

2760

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0810

Hom.:

1769

Bravo

AF:

0.0665

TwinsUK

AF:

0.0809

AC:

300

ALSPAC

AF:

0.0789

AC:

304

ESP6500AA

AF:

0.0172

AC:

ESP6500EA

AF:

0.0807

AC:

694

ExAC

AF:

0.100

AC:

12155

EpiCase

AF:

0.0879

EpiControl

AF:

0.0887

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.25

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.58

Eigen

Pathogenic

0.70

Eigen_PC

Uncertain

0.62

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Benign

0.81

MetaRNN

Benign

0.0024

MetaSVM

Benign

-0.89

MutationAssessor

Pathogenic

3.4

PhyloP100

6.4

PrimateAI

Benign

0.41

PROVEAN

Pathogenic

-5.4

REVEL

Uncertain

0.38

Sift

Uncertain

0.0020

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.33

MPC

0.47

ClinPred

0.031

GERP RS

5.8

Varity_R

0.57

gMVP

0.65

Mutation Taster

=86/14

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs1609860

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over