NM_000047.3:c.1727C>T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000047.3(ARSL):c.1727C>T(p.Pro576Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,196,620 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000047.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000900 AC: 1AN: 111086Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33296
GnomAD3 exomes AF: 0.00000571 AC: 1AN: 175220Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 60508
GnomAD4 exome AF: 0.0000111 AC: 12AN: 1085482Hom.: 0 Cov.: 29 AF XY: 0.00000284 AC XY: 1AN XY: 352732
GnomAD4 genome AF: 0.00000900 AC: 1AN: 111138Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33358
ClinVar
Submissions by phenotype
Chondrodysplasia punctata, brachytelephalangic, autosomal Uncertain:1
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 576 of the ARSE protein (p.Pro576Leu). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with ARSE-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ARSE protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at