22-35660097-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030641.4(APOL6):c.*501A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0851 in 160,098 control chromosomes in the GnomAD database, including 924 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 0.087 (902 hom., cov: 32)
  • Exomes 𝑓: 0.051 (22 hom.)
• Consequence: APOL6 NM_030641.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

Genes affected

APOL6 (HGNC:14870): (apolipoprotein L6) 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOL6	NM_030641.4	c.*501A>T		3_prime_UTR_variant	3/3	ENST00000409652.5
APOL6	XM_011530392.4	c.*501A>T		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOL6	ENST00000409652.5	c.*501A>T		3_prime_UTR_variant	3/3	1	NM_030641.4	P1

Frequencies

GnomAD3 genomes AF: 0.0868 AC: 13205 AN: 152146 Hom.: 894 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0420

Gnomad OTH AF: 0.0841

GnomAD4 exome AF: 0.0507 AC: 397 AN: 7834 Hom.: 22 Cov.: 0 AF XY: 0.0564 AC XY: 234 AN XY: 4146

Gnomad4 AFR exome AF: 0.222

Gnomad4 AMR exome AF: 0.0407

Gnomad4 ASJ exome AF: 0.0862

Gnomad4 EAS exome AF: 0.183

Gnomad4 SAS exome AF: 0.0662

Gnomad4 FIN exome AF: 0.0500

Gnomad4 NFE exome AF: 0.0341

Gnomad4 OTH exome AF: 0.0658

GnomAD4 genome AF: 0.0869 AC: 13233 AN: 152264 Hom.: 902 Cov.: 32 AF XY: 0.0869 AC XY: 6468 AN XY: 74452

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0600

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0731

Gnomad4 FIN AF: 0.0368

Gnomad4 NFE AF: 0.0420

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0209 Hom.: 14

Bravo AF: 0.0938

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs5999924; hg19: chr22-36056144;