3-52502648-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_015136.3(STAB1):c.504C>T(p.His168=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0063 in 1,613,310 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0050 ( 4 hom., cov: 33)
Exomes 𝑓: 0.0064 ( 70 hom. )
Consequence
STAB1
NM_015136.3 synonymous
NM_015136.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.79
Genes affected
STAB1 (HGNC:18628): (stabilin 1) 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, 16 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 endocytose ligands such as low density lipoprotein, Gram-positive and Gram-negative bacteria, and advanced glycosylation end products. Supporting its possible role as a scavenger receptor, the protein rapidly cycles between the plasma membrane and early endosomes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 3-52502648-C-T is Benign according to our data. Variant chr3-52502648-C-T is described in ClinVar as [Benign]. Clinvar id is 767910.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2.79 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00503 (767/152338) while in subpopulation SAS AF= 0.023 (111/4828). AF 95% confidence interval is 0.0195. There are 4 homozygotes in gnomad4. There are 398 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAB1 | NM_015136.3 | c.504C>T | p.His168= | synonymous_variant | 6/69 | ENST00000321725.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAB1 | ENST00000321725.10 | c.504C>T | p.His168= | synonymous_variant | 6/69 | 1 | NM_015136.3 | P1 | |
STAB1 | ENST00000481607.1 | n.559C>T | non_coding_transcript_exon_variant | 6/21 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00506 AC: 770AN: 152220Hom.: 4 Cov.: 33
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GnomAD3 exomes AF: 0.00630 AC: 1579AN: 250594Hom.: 13 AF XY: 0.00733 AC XY: 995AN XY: 135674
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GnomAD4 exome AF: 0.00644 AC: 9402AN: 1460972Hom.: 70 Cov.: 32 AF XY: 0.00699 AC XY: 5076AN XY: 726682
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GnomAD4 genome AF: 0.00503 AC: 767AN: 152338Hom.: 4 Cov.: 33 AF XY: 0.00534 AC XY: 398AN XY: 74484
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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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at