NM_001386885.1:c.323_324delAG

Variant names:

• chr22-36191797-ACT-A
• rs5845253
• NM_001386885.1:c.323_324delAG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001386885.1(APOL4):​c.323_324delAG​(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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 10 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
APOL4	NM_001386885.1	c.323_324delAG	p.Glu108ValfsTer21	frameshift_variant	Exon 4 of 4	ENST00000683024.1	NP_001373814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOL4	ENST00000683024.1	c.323_324delAG	p.Glu108ValfsTer21	frameshift_variant	Exon 4 of 4		NM_001386885.1	ENSP00000507418.1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61239 AN: 151702 Hom.: 13508 Cov.: 0

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

African (AFR) AF: 0.224 AC: 7500 AN: 33480

American (AMR) AF: 0.444 AC: 19847 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 13290 AN: 26136

East Asian (EAS) AF: 0.184 AC: 7308 AN: 39698

South Asian (SAS) AF: 0.449 AC: 38687 AN: 86258

European-Finnish (FIN) AF: 0.448 AC: 23912 AN: 53366

Middle Eastern (MID) AF: 0.516 AC: 2978 AN: 5768

European-Non Finnish (NFE) AF: 0.510 AC: 567559 AN: 1111858

Other (OTH) AF: 0.470 AC: 28368 AN: 60372

GnomAD4 genome AF: 0.404 AC: 61298 AN: 151822 Hom.: 13527 Cov.: 0 AF XY: 0.400 AC XY: 29667 AN XY: 74198

African (AFR) AF: 0.233 AC: 9636 AN: 41394

American (AMR) AF: 0.418 AC: 6375 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1777 AN: 3464

East Asian (EAS) AF: 0.182 AC: 934 AN: 5144

South Asian (SAS) AF: 0.427 AC: 2057 AN: 4814

European-Finnish (FIN) AF: 0.443 AC: 4670 AN: 10536

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34454 AN: 67906

Other (OTH) AF: 0.435 AC: 916 AN: 2104

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
PhyloP100		-0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5845253; hg19: chr22-36587845;