Variant rs5845253 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001386885.1(APOL4):c.323_324del(p.Glu108ValfsTer21) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 1,613,480 control chromosomes in the GnomAD database, including 190,083 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.40 ( 13527 hom., cov: 0)

Exomes 𝑓: 0.49 ( 176556 hom. )

Consequence

APOL4
NM_001386885.1 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.263

Variant links:

Genes affected

APOL4 (HGNC:14867): (apolipoprotein L4) This gene encodes a member of the apolipoprotein L family. The encoded protein 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. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2020]

APOL4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOL4	NM_001386885.1 linkuse as main transcript	c.323_324del	p.Glu108ValfsTer21	frameshift_variant	4/4	ENST00000683024.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOL4	ENST00000683024.1 linkuse as main transcript	c.323_324del	p.Glu108ValfsTer21	frameshift_variant	4/4		NM_001386885.1	P2	Q9BPW4-2

Frequencies

GnomAD3 genomes

AF:

0.404

AC:

61239

AN:

151702

Hom.:

13508

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.369

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.513

Gnomad EAS

AF:

0.181

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.443

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.507

Gnomad OTH

AF:

0.433

GnomAD4 exome

AF:

0.485

AC:

709449

AN:

1461658

Hom.:

176556

AF XY:

0.485

AC XY:

352983

AN XY:

727112

show subpopulations

Gnomad4 AFR exome

AF:

0.224

Gnomad4 AMR exome

AF:

0.444

Gnomad4 ASJ exome

AF:

0.508

Gnomad4 EAS exome

AF:

0.184

Gnomad4 SAS exome

AF:

0.449

Gnomad4 FIN exome

AF:

0.448

Gnomad4 NFE exome

AF:

0.510

Gnomad4 OTH exome

AF:

0.470

GnomAD4 genome

AF:

0.404

AC:

61298

AN:

151822

Hom.:

13527

Cov.:

AF XY:

0.400

AC XY:

29667

AN XY:

74198

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.418

Gnomad4 ASJ

AF:

0.513

Gnomad4 EAS

AF:

0.182

Gnomad4 SAS

AF:

0.427

Gnomad4 FIN

AF:

0.443

Gnomad4 NFE

AF:

0.507

Gnomad4 OTH

AF:

0.435

Alfa

AF:

0.224

Hom.:

1777

Bravo

AF:

0.395

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over