2-42769819-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012205.3(HAAO):c.524G>C(p.Arg175Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,752 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R175Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_012205.3 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 |
---|---|---|---|---|---|---|---|
HAAO | NM_012205.3 | c.524G>C | p.Arg175Pro | missense_variant | 7/10 | ENST00000294973.11 | |
HAAO | XM_011532729.4 | c.434G>C | p.Arg145Pro | missense_variant | 6/9 | ||
HAAO | XM_011532730.4 | c.422G>C | p.Arg141Pro | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAAO | ENST00000294973.11 | c.524G>C | p.Arg175Pro | missense_variant | 7/10 | 1 | NM_012205.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250658Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135454
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461474Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 727034
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74468
ClinVar
Submissions by phenotype
Vertebral, cardiac, renal, and limb defects syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jul 25, 2022 | This variant was identified as compound heterozygous with NM_012205.3:c.431T>C._x000D_ Criteria applied: PM2_SUP - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at