NM_021828.5:c.1682G>A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_021828.5(HPSE2):c.1682G>A(p.Arg561His) variant causes a missense change. The variant allele was found at a frequency of 0.0000217 in 1,614,062 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. R561S) has been classified as Uncertain significance.
Frequency
Consequence
NM_021828.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250748Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135696
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461812Hom.: 0 Cov.: 37 AF XY: 0.0000206 AC XY: 15AN XY: 727202
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74458
ClinVar
Submissions by phenotype
Urofacial syndrome type 1 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at