rs2010467

Variant names:

• chr22-36232861-T-C
• rs2010467
• NM_030882.4:c.10+292A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030882.4(APOL2):​c.10+292A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 150,822 control chromosomes in the GnomAD database, including 29,493 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 0.61 (29493 hom., cov: 26)
• Consequence: APOL2 NM_030882.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 6 publications found

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]

APOL2 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: AD Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOL2	NM_030882.4	c.10+292A>G		intron_variant	Intron 3 of 4	ENST00000358502.10	NP_112092.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOL2	ENST00000358502.10	c.10+292A>G		intron_variant	Intron 3 of 4	1	NM_030882.4	ENSP00000351292.5

Frequencies

GnomAD3 genomes AF: 0.613 AC: 92335 AN: 150704 Hom.: 29454 Cov.: 26

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.0751

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.613 AC: 92429 AN: 150822 Hom.: 29493 Cov.: 26 AF XY: 0.608 AC XY: 44758 AN XY: 73664

African (AFR) AF: 0.556 AC: 22780 AN: 40982

American (AMR) AF: 0.596 AC: 9050 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2219 AN: 3456

East Asian (EAS) AF: 0.0757 AC: 387 AN: 5112

South Asian (SAS) AF: 0.448 AC: 2125 AN: 4740

European-Finnish (FIN) AF: 0.671 AC: 6975 AN: 10390

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.691 AC: 46740 AN: 67674

Other (OTH) AF: 0.619 AC: 1293 AN: 2090

Alfa AF: 0.665 Hom.: 17402

Bravo AF: 0.606

Asia WGS AF: 0.290 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.50
PhyloP100		0.43
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2010467; hg19: chr22-36628907;