dbSNP rs12229292: STAB2:c.7248+582G>T (chr12-103759855-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

-12

BP4_StrongBA1

The NM_017564.10(STAB2):c.7248+582G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,162 control chromosomes in the GnomAD database, including 4,625 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 0.23 ( 4625 hom., cov: 33)

Consequence

STAB2
NM_017564.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0720

Publications

5 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:

ENSG00000257681 (HGNC:58447):

ENSG00000257681 links:

NT5DC3 (HGNC:30826): (5'-nucleotidase domain containing 3) Predicted to enable 5'-nucleotidase activity. Predicted to be involved in dephosphorylation. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

NT5DC3 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 (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAB2	NM_017564.10 link	c.7248+582G>T		intron_variant	Intron 65 of 68	ENST00000388887.7	NP_060034.9	Q8WWQ8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
STAB2	ENST00000388887.7 link	c.7248+582G>T	intron_variant	Intron 65 of 68	1	NM_017564.10	ENSP00000373539.2	Q8WWQ8
STAB2	ENST00000548579.1 link	n.506+582G>T	intron_variant	Intron 2 of 2	4
ENSG00000257681	ENST00000551299.1 link	n.172+6880C>A	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35533

AN:

152044

Hom.:

4620

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.434

Gnomad SAS

AF:

0.434

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.246

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

GnomAD4 genome

AF:

0.234

AC:

35546

AN:

152162

Hom.:

4625

Cov.:

AF XY:

0.238

AC XY:

17708

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.139

AC:

5779

AN:

41520

American (AMR)

AF:

0.268

AC:

4093

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

1020

AN:

3470

East Asian (EAS)

AF:

0.433

AC:

2240

AN:

5174

South Asian (SAS)

AF:

0.434

AC:

2094

AN:

4824

European-Finnish (FIN)

AF:

0.202

AC:

2142

AN:

10586

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.255

AC:

17346

AN:

67996

Other (OTH)

AF:

0.251

AC:

528

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1370

2740

4111

5481

6851

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.253

Hom.:

6111

Bravo

AF:

0.232

Asia WGS

AF:

0.429

AC:

1491

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

1.1

(source)

DANN

Benign

0.74

PhyloP100

-0.072

Mutation Taster

=100/0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over