Variant chr22-36191797-A-ACT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001386885.1(APOL4):c.324_325insAG(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

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

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 Likely_benign. Variant got -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/exons	MANE	UniProt
APOL4	NM_001386885.1 linkuse as main transcript	c.324_325insAG	p.Phe109SerfsTer13	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.324_325insAG	p.Phe109SerfsTer13	frameshift_variant	4/4		NM_001386885.1	P2	Q9BPW4-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.556

AC:

138429

AN:

249174

Hom.:

39909

AF XY:

0.550

AC XY:

74299

AN XY:

135172

show subpopulations

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 SAS exome

AF:

0.556

Gnomad FIN exome

AF:

0.555

Gnomad NFE exome

AF:

0.487

Gnomad OTH exome

AF:

0.532

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

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

Jun 26, 2017

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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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over