12-103640541-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017564.10(STAB2):​c.1040+285C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,894 control chromosomes in the GnomAD database, including 16,626 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 0.46 ( 16626 hom., cov: 32)

Consequence

STAB2
NM_017564.10 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.255
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]

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 (BayesDel_noAF=-0.64).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
STAB2NM_017564.10 linkc.1040+285C>T intron_variant ENST00000388887.7 NP_060034.9 Q8WWQ8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
STAB2ENST00000388887.7 linkc.1040+285C>T intron_variant 1 NM_017564.10 ENSP00000373539.2 Q8WWQ8

Frequencies

GnomAD3 genomes
AF:
0.459
AC:
69601
AN:
151776
Hom.:
16620
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.357
Gnomad AMI
AF:
0.688
Gnomad AMR
AF:
0.427
Gnomad ASJ
AF:
0.474
Gnomad EAS
AF:
0.318
Gnomad SAS
AF:
0.289
Gnomad FIN
AF:
0.506
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.539
Gnomad OTH
AF:
0.451
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.458
AC:
69616
AN:
151894
Hom.:
16626
Cov.:
32
AF XY:
0.453
AC XY:
33654
AN XY:
74236
show subpopulations
Gnomad4 AFR
AF:
0.357
Gnomad4 AMR
AF:
0.427
Gnomad4 ASJ
AF:
0.474
Gnomad4 EAS
AF:
0.318
Gnomad4 SAS
AF:
0.290
Gnomad4 FIN
AF:
0.506
Gnomad4 NFE
AF:
0.539
Gnomad4 OTH
AF:
0.445
Alfa
AF:
0.394
Hom.:
3571
Bravo
AF:
0.451
Asia WGS
AF:
0.253
AC:
878
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
CADD
Benign
12
DANN
Benign
0.73

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.

Other links and lift over

dbSNP: rs1650123; hg19: chr12-104034319; COSMIC: COSV66348106; API