22-35659159-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030641.4(APOL6):c.595A>C(p.Asn199His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,614,090 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030641.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOL6 | NM_030641.4 | c.595A>C | p.Asn199His | missense_variant | 3/3 | ENST00000409652.5 | |
APOL6 | XM_011530392.4 | c.595A>C | p.Asn199His | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOL6 | ENST00000409652.5 | c.595A>C | p.Asn199His | missense_variant | 3/3 | 1 | NM_030641.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251166Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135732
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461886Hom.: 1 Cov.: 32 AF XY: 0.0000866 AC XY: 63AN XY: 727246
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2022 | The c.595A>C (p.N199H) alteration is located in exon 3 (coding exon 2) of the APOL6 gene. This alteration results from a A to C substitution at nucleotide position 595, causing the asparagine (N) at amino acid position 199 to be replaced by a histidine (H). 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