22-36227658-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030882.4(APOL2):c.760G>A(p.Gly254Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030882.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOL2 | NM_030882.4 | c.760G>A | p.Gly254Ser | missense_variant | Exon 5 of 5 | ENST00000358502.10 | NP_112092.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOL2 | ENST00000358502.10 | c.760G>A | p.Gly254Ser | missense_variant | Exon 5 of 5 | 1 | NM_030882.4 | ENSP00000351292.5 | ||
APOL2 | ENST00000249066.10 | c.760G>A | p.Gly254Ser | missense_variant | Exon 6 of 6 | 1 | ENSP00000249066.6 | |||
APOL2 | ENST00000451256.6 | c.1096G>A | p.Gly366Ser | missense_variant | Exon 6 of 6 | 2 | ENSP00000403153.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249506Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135350
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461884Hom.: 0 Cov.: 35 AF XY: 0.0000206 AC XY: 15AN XY: 727242
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.760G>A (p.G254S) alteration is located in exon 6 (coding exon 3) of the APOL2 gene. This alteration results from a G to A substitution at nucleotide position 760, causing the glycine (G) at amino acid position 254 to be replaced by a serine (S). 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