Variant chr12-103654676-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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 nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
STAB2	NM_017564.10 link	c.1529C>A	p.Pro510His	missense_variant	13/69	ENST00000388887.7	NP_060034.9	Q8WWQ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAB2	ENST00000388887.7 link	c.1529C>A	p.Pro510His	missense_variant	13/69	1	NM_017564.10	ENSP00000373539.2		Q8WWQ8

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

GnomAD3 exomes

AF:

0.102

AC:

25516

AN:

251072

Hom.:

1528

AF XY:

0.106

AC XY:

14372

AN XY:

135698

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 SAS exome

AF:

0.160

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

Gnomad4 AFR exome

AF:

0.0127

Gnomad4 AMR exome

AF:

0.102

Gnomad4 ASJ exome

AF:

0.0807

Gnomad4 EAS exome

AF:

0.138

Gnomad4 SAS exome

AF:

0.163

Gnomad4 FIN exome

AF:

0.171

Gnomad4 NFE exome

AF:

0.0822

Gnomad4 OTH exome

AF:

0.101

GnomAD4 genome

AF:

0.0781

AC:

11884

AN:

152242

Hom.:

636

Cov.:

AF XY:

0.0848

AC XY:

6316

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0151

Gnomad4 AMR

AF:

0.103

Gnomad4 ASJ

AF:

0.0804

Gnomad4 EAS

AF:

0.114

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.184

Gnomad4 NFE

AF:

0.0858

Gnomad4 OTH

AF:

0.0979

Alfa

AF:

0.0832

Hom.:

1209

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

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

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

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

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