chrX-72129904-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001024455.4(RTL5):āc.1637G>Cā(p.Arg546Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,208,377 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R546H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001024455.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000897 AC: 1AN: 111501Hom.: 0 Cov.: 24 AF XY: 0.0000297 AC XY: 1AN XY: 33705
GnomAD3 exomes AF: 0.00000558 AC: 1AN: 179244Hom.: 0 AF XY: 0.0000153 AC XY: 1AN XY: 65364
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1096876Hom.: 0 Cov.: 38 AF XY: 0.00000276 AC XY: 1AN XY: 362368
GnomAD4 genome AF: 0.00000897 AC: 1AN: 111501Hom.: 0 Cov.: 24 AF XY: 0.0000297 AC XY: 1AN XY: 33705
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at