18-13746289-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003799.3(RNMT):c.1209T>G(p.Ile403Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,423,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003799.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000842 AC: 2AN: 237614Hom.: 0 AF XY: 0.00000775 AC XY: 1AN XY: 129048
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1423664Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 710208
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1209T>G (p.I403M) alteration is located in exon 9 (coding exon 7) of the RNMT gene. This alteration results from a T to G substitution at nucleotide position 1209, causing the isoleucine (I) at amino acid position 403 to be replaced by a methionine (M). 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