rs2003813

Positions:

• chr22-36232947-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030882.4(APOL2):​c.10+206G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,766 control chromosomes in the GnomAD database, including 6,368 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6368 hom., cov: 30)
• Consequence: APOL2 NM_030882.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

APOL2 (HGNC:619): (apolipoprotein L2) This gene is a member of the apolipoprotein L gene family. The encoded protein is found in the cytoplasm, where it may affect the movement of lipids or allow the binding of lipids to organelles. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOL2	NM_030882.4	c.10+206G>A		intron_variant		ENST00000358502.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOL2	ENST00000358502.10	c.10+206G>A		intron_variant		1	NM_030882.4	P2

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41513 AN: 151646 Hom.: 6362 Cov.: 30

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.00310

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.274 AC: 41522 AN: 151766 Hom.: 6368 Cov.: 30 AF XY: 0.273 AC XY: 20275 AN XY: 74176

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.00310

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.264

Alfa AF: 0.315 Hom.: 997

Bravo AF: 0.260

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs2003813; hg19: chr22-36628993;