dbSNP rs4981021: STAB2:c.6987+503C>T (chr12-103756221-C-T) – 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.6987+503C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,100 control chromosomes in the GnomAD database, including 5,103 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 0.24 ( 5103 hom., cov: 33)

Consequence

STAB2
NM_017564.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.986

Publications

11 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAB2	NM_017564.10 link	c.6987+503C>T		intron_variant	Intron 63 of 68	ENST00000388887.7	NP_060034.9	Q8WWQ8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
STAB2	ENST00000388887.7 link	c.6987+503C>T	intron_variant	Intron 63 of 68	1	NM_017564.10	ENSP00000373539.2	Q8WWQ8
STAB2	ENST00000548073.1 link	n.483+503C>T	intron_variant	Intron 2 of 2	5
ENSG00000257681	ENST00000551299.1 link	n.173-9582G>A	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37208

AN:

151982

Hom.:

5097

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.262

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.484

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.259

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

GnomAD4 genome

AF:

0.245

AC:

37225

AN:

152100

Hom.:

5103

Cov.:

AF XY:

0.250

AC XY:

18579

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.137

AC:

5680

AN:

41482

American (AMR)

AF:

0.271

AC:

4146

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.301

AC:

1044

AN:

3472

East Asian (EAS)

AF:

0.483

AC:

2495

AN:

5170

South Asian (SAS)

AF:

0.425

AC:

2051

AN:

4828

European-Finnish (FIN)

AF:

0.255

AC:

2699

AN:

10572

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.268

AC:

18217

AN:

67982

Other (OTH)

AF:

0.264

AC:

556

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1391

2782

4173

5564

6955

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.267

Hom.:

23847

Bravo

AF:

0.240

Asia WGS

AF:

0.446

AC:

1550

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.3

(source)

DANN

Benign

0.59

PhyloP100

-0.99

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