rs1540297

Positions:

• chr22-35714418-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

APOL5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
APOL5	XM_006724321.5	c.31+680T>C		intron_variant			XP_006724384.1
APOL5	XM_017028945.3	c.-14+680T>C		intron_variant			XP_016884434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.429

Alfa AF: 0.388 Hom.: 8855

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1540297; hg19: chr22-36110465;