22-36191797-ACT-ACTCT

Variant names:

• chr22-36191797-A-ACT
• rs5845253
• NM_001386885.1:c.323_324dupAG

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001386885.1(APOL4):​c.323_324dupAG​(p.Phe109SerfsTer13) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: APOL4 NM_001386885.1 frameshift
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant 22-36191797-A-ACT is Benign according to our data. Variant chr22-36191797-A-ACT is described in ClinVar as [Likely_benign]. Clinvar id is 445778.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOL4	NM_001386885.1	c.323_324dupAG	p.Phe109SerfsTer13	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_324dupAG	p.Phe109SerfsTer13	frameshift_variant	Exon 4 of 4		NM_001386885.1	ENSP00000507418.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD2 exomes AF: 0.556 AC: 138429 AN: 249174 AF XY: 0.550

Gnomad AFR exome AF: 0.773

Gnomad AMR exome AF: 0.559

Gnomad ASJ exome AF: 0.485

Gnomad EAS exome AF: 0.835

Gnomad FIN exome AF: 0.555

Gnomad NFE exome AF: 0.487

Gnomad OTH exome AF: 0.532

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

Alfa AF: 0.248 Hom.: 1777

Asia WGS AF: 0.697 AC: 2417 AN: 3478

EpiCase AF: 0.486

EpiControl AF: 0.487

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 26, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;