XM_006724321.5:c.31+680T>C

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;