rs5999924
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_030641.4(APOL6):c.*501A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 160,130 control chromosomes in the GnomAD database, including 29 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 0.011 ( 29 hom., cov: 32)
Exomes 𝑓: 0.0010 ( 0 hom. )
Consequence
APOL6
NM_030641.4 3_prime_UTR
NM_030641.4 3_prime_UTR
Scores
2
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0107 (1633/152290) while in subpopulation AFR AF= 0.0367 (1523/41532). AF 95% confidence interval is 0.0351. There are 29 homozygotes in gnomad4. There are 748 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 29 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOL6 | NM_030641.4 | c.*501A>G | 3_prime_UTR_variant | 3/3 | ENST00000409652.5 | ||
APOL6 | XM_011530392.4 | c.*501A>G | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOL6 | ENST00000409652.5 | c.*501A>G | 3_prime_UTR_variant | 3/3 | 1 | NM_030641.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0107 AC: 1622AN: 152172Hom.: 27 Cov.: 32
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GnomAD4 exome AF: 0.00102 AC: 8AN: 7840Hom.: 0 Cov.: 0 AF XY: 0.000964 AC XY: 4AN XY: 4148
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GnomAD4 genome ? AF: 0.0107 AC: 1633AN: 152290Hom.: 29 Cov.: 32 AF XY: 0.0100 AC XY: 748AN XY: 74464
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at