Variant 12-103631668-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_017564.10(STAB2):c.558G>A(p.Ala186=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00743 in 1,614,164 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0052 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0077 ( 48 hom. )

Consequence

STAB2
NM_017564.10 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -6.04

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 -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 12-103631668-G-A is Benign according to our data. Variant chr12-103631668-G-A is described in ClinVar as [Benign]. Clinvar id is 775099.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-6.04 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAB2	NM_017564.10 linkuse as main transcript	c.558G>A	p.Ala186=	synonymous_variant	6/69	ENST00000388887.7	NP_060034.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAB2	ENST00000388887.7 linkuse as main transcript	c.558G>A	p.Ala186=	synonymous_variant	6/69	1	NM_017564.10	ENSP00000373539	P1

Frequencies

GnomAD3 genomes

AF:

0.00523

AC:

796

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.00613

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00875

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00629

AC:

1581

AN:

251410

Hom.:

AF XY:

0.00643

AC XY:

873

AN XY:

135872

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00318

Gnomad ASJ exome

AF:

0.00169

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00448

Gnomad FIN exome

AF:

0.00901

Gnomad NFE exome

AF:

0.00931

Gnomad OTH exome

AF:

0.00700

GnomAD4 exome

AF:

0.00766

AC:

11198

AN:

1461864

Hom.:

Cov.:

AF XY:

0.00758

AC XY:

5509

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.00114

Gnomad4 AMR exome

AF:

0.00335

Gnomad4 ASJ exome

AF:

0.00142

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00486

Gnomad4 FIN exome

AF:

0.0100

Gnomad4 NFE exome

AF:

0.00860

Gnomad4 OTH exome

AF:

0.00687

GnomAD4 genome

AF:

0.00523

AC:

796

AN:

152300

Hom.:

Cov.:

AF XY:

0.00459

AC XY:

342

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00108

Gnomad4 AMR

AF:

0.00366

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.00613

Gnomad4 NFE

AF:

0.00875

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00775

Hom.:

Bravo

AF:

0.00509

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.00796

EpiControl

AF:

0.00960

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.86

DANN

Benign

0.25

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over