22-36227882-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030882.4(APOL2):c.536C>T(p.Ala179Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOL2 | NM_030882.4 | c.536C>T | p.Ala179Val | missense_variant | 5/5 | ENST00000358502.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOL2 | ENST00000358502.10 | c.536C>T | p.Ala179Val | missense_variant | 5/5 | 1 | NM_030882.4 | P2 | |
APOL2 | ENST00000249066.10 | c.536C>T | p.Ala179Val | missense_variant | 6/6 | 1 | P2 | ||
APOL2 | ENST00000451256.6 | c.872C>T | p.Ala291Val | missense_variant | 6/6 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249370Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135298
GnomAD4 exome AF: 0.0000711 AC: 104AN: 1461888Hom.: 0 Cov.: 35 AF XY: 0.0000550 AC XY: 40AN XY: 727242
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.536C>T (p.A179V) alteration is located in exon 6 (coding exon 3) of the APOL2 gene. This alteration results from a C to T substitution at nucleotide position 536, causing the alanine (A) at amino acid position 179 to be replaced by a valine (V). 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