rs71785313
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM4BA1
The ENST00000397278.8(APOL1):c.1164_1169del(p.Asn388_Tyr389del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00701 in 1,612,914 control chromosomes in the GnomAD database, including 748 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity,risk factor (no stars).
Frequency
Genomes: 𝑓 0.039 ( 410 hom., cov: 31)
Exomes 𝑓: 0.0037 ( 338 hom. )
Consequence
APOL1
ENST00000397278.8 inframe_deletion
ENST00000397278.8 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.259
Genes affected
APOL1 (HGNC:618): (apolipoprotein L1) This gene encodes a secreted high density lipoprotein which binds to apolipoprotein A-I. Apolipoprotein A-I is a relatively abundant plasma protein and is the major apoprotein of HDL. It is involved in the formation of most cholesteryl esters in plasma and also promotes efflux of cholesterol from cells. This apolipoprotein L family member may play a role in lipid exchange and transport throughout the body, as well as in reverse cholesterol transport from peripheral cells to the liver. Several different transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in ENST00000397278.8.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOL1 | NM_003661.4 | c.1164_1169del | p.Asn388_Tyr389del | inframe_deletion | 6/6 | ENST00000397278.8 | NP_003652.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOL1 | ENST00000397278.8 | c.1164_1169del | p.Asn388_Tyr389del | inframe_deletion | 6/6 | 1 | NM_003661.4 | ENSP00000380448 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0388 AC: 5899AN: 152120Hom.: 410 Cov.: 31
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GnomAD3 exomes AF: 0.00976 AC: 2429AN: 248746Hom.: 144 AF XY: 0.00713 AC XY: 961AN XY: 134836
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GnomAD4 exome AF: 0.00369 AC: 5397AN: 1460676Hom.: 338 AF XY: 0.00303 AC XY: 2204AN XY: 726584
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GnomAD4 genome AF: 0.0388 AC: 5908AN: 152238Hom.: 410 Cov.: 31 AF XY: 0.0378 AC XY: 2815AN XY: 74452
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ClinVar
Significance: Conflicting classifications of pathogenicity; risk factor
Submissions summary: Pathogenic:3Uncertain:1Benign:2Other:3
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Focal segmental glomerulosclerosis 4, susceptibility to Pathogenic:1Other:2
risk factor, no assertion criteria provided | literature only | OMIM | Aug 13, 2010 | - - |
risk factor, criteria provided, single submitter | clinical testing | Molecular Diagnostics Lab, Nemours Children's Health, Delaware | Feb 27, 2015 | G2 - |
Likely risk allele, criteria provided, single submitter | clinical testing | Mendelics | Mar 24, 2023 | - - |
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 07, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | This variant, c.1164_1169del, results in the deletion of 2 amino acid(s) of the APOL1 protein (p.Asn388_Tyr389del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs143830837, gnomAD 14%), and has an allele count higher than expected for a pathogenic variant. This variant constitutes the “G2” allele of APOL1. This allele is associated with increased risk for several forms of kidney disease in individuals of African-American ancestry when present in homozygosity or in trans with the “G1” allele (which is composed of the c.1024A>G (p.Ser342Gly) and c.1152T>G (p.Ile384Met) variants in cis). Several large case-control studies have shown a 6- to 47-fold increased risk of focal segmental glomerulosclerosis, HIV-associated nephropathy, or non-diabetic end-stage kidney disease in individuals with homozygous G1, homozygous G2, or G1 in trans with G2 alleles (PMID: 20647424, 20635188, 21997394). Similar studies in African populations have generally recapitulated these findings, but these studies are based on a relatively small number of individuals (PMID: 30340464, 25788523). A recent PheWAS study also appears to support these findings, although the risk of end-stage kidney disease may be smaller than initially assumed (closer to 3- to 4-fold; PMID: 32247630). ClinVar contains an entry for this variant (Variation ID: 6081). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on APOL1 function (PMID: 30332315, 32675303). In summary, this variant has been shown to confer an increased risk for kidney disease, either in homozygosity or in trans with the G1 allele. However, its significance when present in heterozygosity is unclear. For these reasons, this change has been classified as a Variant of Uncertain Significance. - |
Nephrotic range proteinuria Pathogenic:1
Pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | - | - - |
Focal segmental glomerulosclerosis Pathogenic:1
Pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 29, 2024 | - - |
Hyalinosis, Segmental Glomerular Other:1
risk factor, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 04, 2020 | APOL1 c.1164_1169del (p.Asn388_Tyr389del), traditionally referred to as G1, has been associated with increased risk for multiple renal diseases in African Americans, particularly focal segmental glomerulosclerosis (FSGS), as well as an increased risk for end-stage kidney disease (ESKD). This variant is common in individuals of African ancestry (14%, Genome Aggregation Database (gnomAD); rs71785313) and is present in ClinVar (ID: 6081). Several small case-control studies have reported odds ratios between 3.92-25.1 for developing FSGS/HIVAN in homozygous individuals (OR=3.92 [95% CI 1.47-9.39] for FSGS/HIVAN Ito 2014, OR=14.4 [95% CI 1.7-116.3] for HIVAN, OR=25.1 [95% CI 8.8-83.3] for FSGS Kopp 2011, OR=5.69 [95% CI not given, P<0.00001] Limou 2015). In vitro and in vivo studies provide some evidence that these alleles impact protein function (Beckerman 2017, Hayek 2017). In summary, this variant is an established risk factor for chronic kidney disease in homozygous state. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at