chr22-35660097-A-T

Variant names:

• chr22-35660097-A-T
• rs5999924
• NM_030641.4:c.*501A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030641.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOL6	NM_030641.4	MANE Select	c.*501A>T		3_prime_UTR	Exon 3 of 3	NP_085144.1	Q9BWW8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOL6	ENST00000409652.5	TSL:1 MANE Select	c.*501A>T		3_prime_UTR	Exon 3 of 3	ENSP00000386280.3	Q9BWW8
	APOL6	ENST00000958488.1		c.*501A>T		3_prime_UTR	Exon 4 of 4	ENSP00000628547.1

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

African (AFR) AF: 0.222 AC: 20 AN: 90

American (AMR) AF: 0.0407 AC: 80 AN: 1966

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 5 AN: 58

East Asian (EAS) AF: 0.183 AC: 70 AN: 382

South Asian (SAS) AF: 0.0662 AC: 61 AN: 922

European-Finnish (FIN) AF: 0.0500 AC: 3 AN: 60

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.0341 AC: 138 AN: 4046

Other (OTH) AF: 0.0658 AC: 20 AN: 304

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

African (AFR) AF: 0.171 AC: 7116 AN: 41518

American (AMR) AF: 0.0600 AC: 918 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1012 AN: 5178

South Asian (SAS) AF: 0.0731 AC: 353 AN: 4832

European-Finnish (FIN) AF: 0.0368 AC: 391 AN: 10618

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0420 AC: 2859 AN: 68024

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0209 Hom.: 14

Bravo AF: 0.0938

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-0.62
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: rs5999924; hg19: chr22-36056144;