chr22-35726319-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030642.1(APOL5):c.251G>A(p.Arg84Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,614,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030642.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOL5 | NM_030642.1 | c.251G>A | p.Arg84Gln | missense_variant | 3/5 | ENST00000249044.2 | |
APOL5 | XM_006724321.5 | c.203G>A | p.Arg68Gln | missense_variant | 4/6 | ||
APOL5 | XM_017028945.3 | c.35G>A | p.Arg12Gln | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOL5 | ENST00000249044.2 | c.251G>A | p.Arg84Gln | missense_variant | 3/5 | 1 | NM_030642.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251338Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135854
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727230
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2023 | The c.251G>A (p.R84Q) alteration is located in exon 3 (coding exon 3) of the APOL5 gene. This alteration results from a G to A substitution at nucleotide position 251, causing the arginine (R) at amino acid position 84 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at