22-35729217-T-G

Variant names:

• chr22-35729217-T-G
• rs2016586
• NM_030642.1:c.*7-137T>G

Variant summary

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

The NM_030642.1(APOL5):​c.*7-137T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 262,200 control chromosomes in the GnomAD database, including 69,461 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 0.74 (42926 hom., cov: 32)
  • Exomes 𝑓: 0.69 (26535 hom.)
• Consequence: APOL5 NM_030642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOL5	NM_030642.1	c.*7-137T>G		intron_variant	Intron 4 of 4	ENST00000249044.2	NP_085145.1
APOL5	XM_006724321.5	c.*7-137T>G		intron_variant	Intron 5 of 5		XP_006724384.1
APOL5	XM_017028945.3	c.*7-137T>G		intron_variant	Intron 4 of 4		XP_016884434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOL5	ENST00000249044.2	c.*7-137T>G		intron_variant	Intron 4 of 4	1	NM_030642.1	ENSP00000249044.2

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112781 AN: 151996 Hom.: 42881 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.752

GnomAD4 exome AF: 0.690 AC: 75949 AN: 110086 Hom.: 26535 AF XY: 0.692 AC XY: 38374 AN XY: 55446

African (AFR) AF: 0.913 AC: 2725 AN: 2986

American (AMR) AF: 0.556 AC: 1216 AN: 2186

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2782 AN: 4070

East Asian (EAS) AF: 0.770 AC: 4311 AN: 5598

South Asian (SAS) AF: 0.758 AC: 5645 AN: 7450

European-Finnish (FIN) AF: 0.602 AC: 4185 AN: 6950

Middle Eastern (MID) AF: 0.780 AC: 476 AN: 610

European-Non Finnish (NFE) AF: 0.679 AC: 49300 AN: 72604

Other (OTH) AF: 0.696 AC: 5309 AN: 7632

GnomAD4 genome AF: 0.742 AC: 112880 AN: 152114 Hom.: 42926 Cov.: 32 AF XY: 0.736 AC XY: 54721 AN XY: 74358

African (AFR) AF: 0.912 AC: 37884 AN: 41532

American (AMR) AF: 0.610 AC: 9309 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2365 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3926 AN: 5178

South Asian (SAS) AF: 0.782 AC: 3772 AN: 4822

European-Finnish (FIN) AF: 0.601 AC: 6341 AN: 10548

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46900 AN: 67974

Other (OTH) AF: 0.752 AC: 1592 AN: 2116

Alfa AF: 0.710 Hom.: 22711

Bravo AF: 0.749

Asia WGS AF: 0.779 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.47
PhyloP100		-0.36
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: rs2016586; hg19: chr22-36125264;