14-100880953-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001134888.3(RTL1):c.3836G>A(p.Arg1279His) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001134888.3 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: 0.00312 AC: 4AN: 1282Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.000138 AC: 6AN: 43424Hom.: 0 AF XY: 0.000125 AC XY: 3AN XY: 23928
GnomAD4 exome AF: 0.00101 AC: 44AN: 43494Hom.: 0 Cov.: 0 AF XY: 0.000677 AC XY: 17AN XY: 25114
GnomAD4 genome AF: 0.00312 AC: 4AN: 1282Hom.: 0 Cov.: 0 AF XY: 0.00378 AC XY: 3AN XY: 794
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3836G>A (p.R1279H) alteration is located in exon 1 (coding exon 1) of the RTL1 gene. This alteration results from a G to A substitution at nucleotide position 3836, causing the arginine (R) at amino acid position 1279 to be replaced by a histidine (H). 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