chr15-41417212-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015138.5(RTF1):c.97C>T(p.Arg33Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000808 in 1,262,138 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 (★).
Frequency
Consequence
NM_015138.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTF1 | ENST00000389629.9 | c.97C>T | p.Arg33Trp | missense_variant | Exon 1 of 18 | 1 | NM_015138.5 | ENSP00000374280.4 | ||
RTF1 | ENST00000462276.1 | n.81C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 4 | |||||
RTF1 | ENST00000558298.5 | n.174+8631C>T | intron_variant | Intron 1 of 2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000711 AC: 1AN: 14072Hom.: 0 AF XY: 0.000148 AC XY: 1AN XY: 6752
GnomAD4 exome AF: 0.0000766 AC: 85AN: 1109882Hom.: 0 Cov.: 31 AF XY: 0.000102 AC XY: 54AN XY: 527816
GnomAD4 genome AF: 0.000112 AC: 17AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74432
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.97C>T (p.R33W) alteration is located in exon 1 (coding exon 1) of the RTF1 gene. This alteration results from a C to T substitution at nucleotide position 97, causing the arginine (R) at amino acid position 33 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