X-3015002-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001011719.2(ARSH):c.373C>T(p.Arg125Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000091 in 1,209,402 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001011719.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000895 AC: 1AN: 111701Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33871
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182193Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66795
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1097701Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 4AN XY: 363065
GnomAD4 genome AF: 0.00000895 AC: 1AN: 111701Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33871
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.373C>T (p.R125W) alteration is located in exon 4 (coding exon 4) of the ARSH gene. This alteration results from a C to T substitution at nucleotide position 373, causing the arginine (R) at amino acid position 125 to be replaced by a tryptophan (W). 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