chr12-103631642-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_017564.10(STAB2):c.532G>A(p.Asp178Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00129 in 1,614,172 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0071 ( 13 hom., cov: 32)
Exomes 𝑓: 0.00069 ( 12 hom. )
Consequence
STAB2
NM_017564.10 missense
NM_017564.10 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 0.785
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009839028).
BP6
?
Variant 12-103631642-G-A is Benign according to our data. Variant chr12-103631642-G-A is described in ClinVar as [Benign]. Clinvar id is 787928.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00707 (1077/152288) while in subpopulation AFR AF= 0.0245 (1016/41542). AF 95% confidence interval is 0.0232. There are 13 homozygotes in gnomad4. There are 483 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAB2 | NM_017564.10 | c.532G>A | p.Asp178Asn | missense_variant | 6/69 | ENST00000388887.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAB2 | ENST00000388887.7 | c.532G>A | p.Asp178Asn | missense_variant | 6/69 | 1 | NM_017564.10 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00706 AC: 1075AN: 152170Hom.: 12 Cov.: 32
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GnomAD3 exomes AF: 0.00174 AC: 437AN: 251470Hom.: 3 AF XY: 0.00134 AC XY: 182AN XY: 135912
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GnomAD4 exome AF: 0.000685 AC: 1002AN: 1461884Hom.: 12 Cov.: 31 AF XY: 0.000612 AC XY: 445AN XY: 727246
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GnomAD4 genome ? AF: 0.00707 AC: 1077AN: 152288Hom.: 13 Cov.: 32 AF XY: 0.00649 AC XY: 483AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 11, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at