rs1540297

Variant names:

• chr22-35714418-T-C
• rs1540297
• XM_006724321.5:c.31+680T>C

Variant summary

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

The XM_006724321.5(APOL5):​c.31+680T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,150 control chromosomes in the GnomAD database, including 14,354 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 0.42 (14354 hom., cov: 33)
• Consequence: APOL5 XM_006724321.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 4 publications found

Genes affected

APOL5 (HGNC:14869): (apolipoprotein L5) 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. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOL5	XM_006724321.5	c.31+680T>C		intron_variant	Intron 2 of 5		XP_006724384.1
APOL5	XM_017028945.3	c.-14+680T>C		intron_variant	Intron 2 of 4		XP_016884434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63632 AN: 152032 Hom.: 14333 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.419 AC: 63700 AN: 152150 Hom.: 14354 Cov.: 33 AF XY: 0.411 AC XY: 30607 AN XY: 74388

African (AFR) AF: 0.580 AC: 24041 AN: 41470

American (AMR) AF: 0.385 AC: 5879 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1391 AN: 3470

East Asian (EAS) AF: 0.139 AC: 722 AN: 5192

South Asian (SAS) AF: 0.333 AC: 1605 AN: 4826

European-Finnish (FIN) AF: 0.315 AC: 3338 AN: 10584

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25392 AN: 68004

Other (OTH) AF: 0.429 AC: 907 AN: 2114

Alfa AF: 0.388 Hom.: 14133

Bravo AF: 0.429

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.44
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1540297; hg19: chr22-36110465;