8-16143708-T-TATA
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_138715.3(MSR1):c.980-98_980-97insTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 828,288 control chromosomes in the GnomAD database, including 9,870 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.14 ( 2543 hom., cov: 30)
Exomes 𝑓: 0.10 ( 7327 hom. )
Consequence
MSR1
NM_138715.3 intron
NM_138715.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0580
Genes affected
MSR1 (HGNC:7376): (macrophage scavenger receptor 1) This gene encodes the class A macrophage scavenger receptors, which include three different types (1, 2, 3) generated by alternative splicing of this gene. These receptors or isoforms are macrophage-specific trimeric integral membrane glycoproteins and have been implicated in many macrophage-associated physiological and pathological processes including atherosclerosis, Alzheimer's disease, and host defense. The isoforms type 1 and type 2 are functional receptors and are able to mediate the endocytosis of modified low density lipoproteins (LDLs). The isoform type 3 does not internalize modified LDL (acetyl-LDL) despite having the domain shown to mediate this function in the types 1 and 2 isoforms. It has an altered intracellular processing and is trapped within the endoplasmic reticulum, making it unable to perform endocytosis. The isoform type 3 can inhibit the function of isoforms type 1 and type 2 when co-expressed, indicating a dominant negative effect and suggesting a mechanism for regulation of scavenger receptor activity in macrophages. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.142 AC: 21558AN: 151840Hom.: 2530 Cov.: 30
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GnomAD4 exome AF: 0.101 AC: 68213AN: 676330Hom.: 7327 AF XY: 0.102 AC XY: 36985AN XY: 361144
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GnomAD4 genome AF: 0.142 AC: 21612AN: 151958Hom.: 2543 Cov.: 30 AF XY: 0.145 AC XY: 10744AN XY: 74294
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ClinVar
Not reported inComputational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at