Variant chr22-36253920-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_145343.3(APOL1):c.-43C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,612,714 control chromosomes in the GnomAD database, including 10,694 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1252 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9442 hom. )

Consequence

APOL1
NM_145343.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.89

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]

APOL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 22-36253920-C-T is Benign according to our data. Variant chr22-36253920-C-T is described in ClinVar as [Benign]. Clinvar id is 1225811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOL1	NM_003661.4 link	c.-20+701C>T		intron_variant		ENST00000397278.8	NP_003652.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOL1	ENST00000397278.8 link	c.-20+701C>T		intron_variant		1	NM_003661.4	ENSP00000380448.4		O14791-1

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18956

AN:

152006

Hom.:

1247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.0986

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.0323

Gnomad SAS

AF:

0.0563

Gnomad FIN

AF:

0.168

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.142

GnomAD3 exomes

AF:

0.106

AC:

26753

AN:

251310

Hom.:

1727

AF XY:

0.105

AC XY:

14239

AN XY:

135832

show subpopulations

Gnomad AFR exome

AF:

0.159

Gnomad AMR exome

AF:

0.0667

Gnomad ASJ exome

AF:

0.136

Gnomad EAS exome

AF:

0.0360

Gnomad SAS exome

AF:

0.0537

Gnomad FIN exome

AF:

0.169

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.118

GnomAD4 exome

AF:

0.109

AC:

159670

AN:

1460590

Hom.:

9442

Cov.:

AF XY:

0.108

AC XY:

78435

AN XY:

726704

show subpopulations

Gnomad4 AFR exome

AF:

0.156

Gnomad4 AMR exome

AF:

0.0710

Gnomad4 ASJ exome

AF:

0.136

Gnomad4 EAS exome

AF:

0.0317

Gnomad4 SAS exome

AF:

0.0557

Gnomad4 FIN exome

AF:

0.163

Gnomad4 NFE exome

AF:

0.113

Gnomad4 OTH exome

AF:

0.111

GnomAD4 genome

AF:

0.125

AC:

18991

AN:

152124

Hom.:

1252

Cov.:

AF XY:

0.125

AC XY:

9284

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.158

Gnomad4 AMR

AF:

0.0986

Gnomad4 ASJ

AF:

0.128

Gnomad4 EAS

AF:

0.0324

Gnomad4 SAS

AF:

0.0553

Gnomad4 FIN

AF:

0.168

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.141

Alfa

AF:

0.110

Hom.:

989

Bravo

AF:

0.125

Asia WGS

AF:

0.0620

AC:

216

AN:

3478

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	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.026

DANN

Benign

0.53

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over