rs73885319

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5BP4BA1

The ENST00000397278.8(APOL1):​c.1024A>G​(p.Ser342Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,614,072 control chromosomes in the GnomAD database, including 2,158 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity,risk factor (no stars).

Frequency

Genomes: 𝑓 0.062 ( 1084 hom., cov: 31)
Exomes 𝑓: 0.0061 ( 1074 hom. )

Consequence

APOL1
ENST00000397278.8 missense

Scores

18

Clinical Significance

Conflicting classifications of pathogenicity; risk factor criteria provided, conflicting classifications P:7U:2O:2

Conservation

PhyloP100: 0.277
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PP5
Variant 22-36265860-A-G is Pathogenic according to our data. Variant chr22-36265860-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity, risk_factor]. Clinvar id is 277678.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_risk_allele=1, risk_factor=2, Uncertain_significance=2}.
BP4
Computational evidence support a benign effect (MetaRNN=0.01211217). . Strength limited to SUPPORTING due to the PP5.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
APOL1NM_003661.4 linkuse as main transcriptc.1024A>G p.Ser342Gly missense_variant 6/6 ENST00000397278.8 NP_003652.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
APOL1ENST00000397278.8 linkuse as main transcriptc.1024A>G p.Ser342Gly missense_variant 6/61 NM_003661.4 ENSP00000380448 A2O14791-1

Frequencies

GnomAD3 genomes
AF:
0.0624
AC:
9495
AN:
152060
Hom.:
1084
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.223
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0132
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000206
Gnomad OTH
AF:
0.0340
GnomAD3 exomes
AF:
0.0161
AC:
4039
AN:
251414
Hom.:
478
AF XY:
0.0116
AC XY:
1574
AN XY:
135896
show subpopulations
Gnomad AFR exome
AF:
0.231
Gnomad AMR exome
AF:
0.00671
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000879
Gnomad OTH exome
AF:
0.00571
GnomAD4 exome
AF:
0.00609
AC:
8910
AN:
1461894
Hom.:
1074
Cov.:
36
AF XY:
0.00524
AC XY:
3810
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.237
Gnomad4 AMR exome
AF:
0.00729
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000162
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000495
Gnomad4 OTH exome
AF:
0.00950
GnomAD4 genome
AF:
0.0624
AC:
9496
AN:
152178
Hom.:
1084
Cov.:
31
AF XY:
0.0593
AC XY:
4410
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.222
Gnomad4 AMR
AF:
0.0131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000206
Gnomad4 OTH
AF:
0.0336
Alfa
AF:
0.0138
Hom.:
370
Bravo
AF:
0.0705
ESP6500AA
AF:
0.226
AC:
994
ESP6500EA
AF:
0.000349
AC:
3
ExAC
AF:
0.0206
AC:
2496
Asia WGS
AF:
0.00837
AC:
30
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000178

ClinVar

Significance: Conflicting classifications of pathogenicity; risk factor
Submissions summary: Pathogenic:7Uncertain:2Other:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Other:1
risk factor, criteria provided, single submitterclinical testingGeneDxFeb 26, 2020This variant is associated with the following publications: (PMID: 28696248, 27650483, 32581362, 21910715, 24379297, 23768513, 24518129, 25993319, 22832513, 24206458, 20635188, 20647424, 30173819, 30315176) -
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 26, 2022This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 342 of the APOL1 protein (p.Ser342Gly). This variant is present in population databases (rs73885319, gnomAD 23%), and has an allele count higher than expected for a pathogenic variant. This variant, along with c.1152T>G (p.Ile384Met), constitutes the “G1” 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 “G2” allele (c.1164_1169delTTATAA (p.Asn388_Tyr389del)). 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). p.Ile384Met and p.Ser342Gly are almost always present on the same allele (in cis), but p.Ser342Gly is thought to be the main driver of increased risk (PMID: 21997394). p.Ile384Met is therefore classified as Benign at Invitae. ClinVar contains an entry for this variant (Variation ID: 277678). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Experimental studies have shown that this missense change affects 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 G2 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 providedresearchNIHR Bioresource Rare Diseases, University of Cambridge-- -
not specified Pathogenic:1
Likely risk allele, criteria provided, single submitterclinical testingMendelicsFeb 15, 2023- -
Glomerulonephritis Pathogenic:1
Pathogenic, no assertion criteria providedresearchNIHR Bioresource Rare Diseases, University of Cambridge-- -
Focal segmental glomerulosclerosis;C2237347:Sickled erythrocytes Pathogenic:1
Pathogenic, no assertion criteria providedresearchNIHR Bioresource Rare Diseases, University of Cambridge-- -
Proteinuria Pathogenic:1
Pathogenic, no assertion criteria providedresearchNIHR Bioresource Rare Diseases, University of Cambridge-- -
Focal segmental glomerulosclerosis Pathogenic:1
Pathogenic, no assertion criteria providedresearchNIHR Bioresource Rare Diseases, University of Cambridge-- -
Focal segmental glomerulosclerosis;C0403397:Steroid-resistant nephrotic syndrome Pathogenic:1
Pathogenic, no assertion criteria providedresearchNIHR Bioresource Rare Diseases, University of Cambridge-- -
APOL1-associated kidney disease Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingClinical Genomics Laboratory, Washington University in St. LouisAug 29, 2023Sequence analysis identified the presence of a single APOL1 risk allele in a heterozygous state (G1). The G1 allele is composed of two missense variants: G1G (p.S342G) and G1M (p.I384M). APOL1 risk alleles occur at high frequency among populations of African ancestry (22-24% and 13-14% for G1 and G2, respectively) and are absent or nearly absent from other populations. Inheriting two risk variants greatly increases risk of kidney disease, whereas inheriting one risk allele confers minimal or no risk (Friedman DJ et al., PMID: 32616495). APOL1-associated kidney disease includes focal segmental glomerulosclerosis, CKD associated with hypertension, HIV, systemic lupus erythematosus (SLE), and sickle cell disease, among others (Friedman DJ et al., PMID: 32616495). -
Hyalinosis, Segmental Glomerular Other:1
risk factor, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 04, 2020See compound het c.[1024A>G;1152T>G] -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.073
BayesDel_addAF
Benign
-0.77
T
BayesDel_noAF
Benign
-0.73
CADD
Benign
0.11
DANN
Benign
0.092
DEOGEN2
Benign
0.026
T;T;.;.;T
Eigen
Benign
-2.1
Eigen_PC
Benign
-2.0
FATHMM_MKL
Benign
0.00018
N
LIST_S2
Benign
0.59
.;.;T;T;T
MetaRNN
Benign
0.012
T;T;T;T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
-1.7
N;N;.;.;N
MutationTaster
Benign
1.0
P;P;P;P;P;P
PrimateAI
Benign
0.25
T
PROVEAN
Benign
4.5
N;N;N;N;N
REVEL
Benign
0.081
Sift
Benign
1.0
T;T;T;T;T
Sift4G
Benign
1.0
T;T;T;T;T
Polyphen
0.0
B;B;.;B;B
Vest4
0.031
MPC
0.056
ClinPred
0.0012
T
GERP RS
-0.38
Varity_R
0.016
gMVP
0.20

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: rs73885319; hg19: chr22-36661906; COSMIC: COSV59869297; COSMIC: COSV59869297; API