chr22-35726744-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.676G>A(p.Ala226Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000979 in 1,614,254 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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.676G>A | p.Ala226Thr | missense_variant | 3/5 | ENST00000249044.2 | |
APOL5 | XM_006724321.5 | c.628G>A | p.Ala210Thr | missense_variant | 4/6 | ||
APOL5 | XM_017028945.3 | c.460G>A | p.Ala154Thr | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOL5 | ENST00000249044.2 | c.676G>A | p.Ala226Thr | missense_variant | 3/5 | 1 | NM_030642.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000473 AC: 72AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251480Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135912
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461894Hom.: 0 Cov.: 74 AF XY: 0.0000440 AC XY: 32AN XY: 727248
GnomAD4 genome ? AF: 0.000492 AC: 75AN: 152360Hom.: 1 Cov.: 33 AF XY: 0.000550 AC XY: 41AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2022 | The c.676G>A (p.A226T) 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 676, causing the alanine (A) at amino acid position 226 to be replaced by a threonine (T). 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