rs5750146

chr22-35660681-G-A

Variant summary

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

The NM_030641.4(APOL6):c.*1085G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 152,704 control chromosomes in the GnomAD database, including 904 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 (903 hom., cov: 32)
  • Exomes 𝑓: 0.087 (1 hom.)
• Consequence: APOL6 NM_030641.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOL6	NM_030641.4	c.*1085G>A		3_prime_UTR_variant	3/3	ENST00000409652.5
APOL6	XM_011530392.4	c.*1085G>A		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOL6	ENST00000409652.5	c.*1085G>A		3_prime_UTR_variant	3/3	1	NM_030641.4	P1

Frequencies

GnomAD3 genomes AF: 0.0868 AC: 13199 AN: 152148 Hom.: 895 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0420

Gnomad OTH AF: 0.0840

GnomAD4 exome AF: 0.0868 AC: 38 AN: 438 Hom.: 1 Cov.: 0 AF XY: 0.112 AC XY: 24 AN XY: 214

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 0.0905

Gnomad4 NFE exome AF: 0.0385

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.0869 AC: 13228 AN: 152266 Hom.: 903 Cov.: 32 AF XY: 0.0869 AC XY: 6466 AN XY: 74448

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0597

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0726

Gnomad4 FIN AF: 0.0368

Gnomad4 NFE AF: 0.0420

Gnomad4 OTH AF: 0.0846

Alfa AF: 0.0529 Hom.: 490

Bravo AF: 0.0917

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.7
Dann	Benign	0.23

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: rs5750146; hg19: chr22-36056728;