X-47081187-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001282848.2(RGN):c.-117C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 1,202,693 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001282848.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000359 AC: 4AN: 111483Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33697
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183404Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67842
GnomAD4 exome AF: 0.00000916 AC: 10AN: 1091161Hom.: 0 Cov.: 28 AF XY: 0.0000112 AC XY: 4AN XY: 356733
GnomAD4 genome AF: 0.0000717 AC: 8AN: 111532Hom.: 0 Cov.: 22 AF XY: 0.000118 AC XY: 4AN XY: 33756
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.43C>T (p.R15W) alteration is located in exon 3 (coding exon 1) of the RGN gene. This alteration results from a C to T substitution at nucleotide position 43, causing the arginine (R) at amino acid position 15 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