9-3225104-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001282116.2(RFX3):c.2188G>A(p.Val730Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0017 in 1,613,946 control chromosomes in the GnomAD database, including 4 homozygotes. 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 Likely benign (no stars).
Frequency
Consequence
NM_001282116.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RFX3 | ENST00000617270.5 | c.2188G>A | p.Val730Ile | missense_variant | Exon 17 of 17 | 2 | NM_001282116.2 | ENSP00000482598.1 | ||
RFX3 | ENST00000382004.7 | c.2188G>A | p.Val730Ile | missense_variant | Exon 18 of 18 | 1 | ENSP00000371434.3 |
Frequencies
GnomAD3 genomes AF: 0.000992 AC: 151AN: 152182Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00120 AC: 300AN: 250858Hom.: 1 AF XY: 0.00119 AC XY: 162AN XY: 135588
GnomAD4 exome AF: 0.00178 AC: 2596AN: 1461646Hom.: 3 Cov.: 31 AF XY: 0.00170 AC XY: 1236AN XY: 727130
GnomAD4 genome AF: 0.000991 AC: 151AN: 152300Hom.: 1 Cov.: 33 AF XY: 0.00110 AC XY: 82AN XY: 74480
ClinVar
Submissions by phenotype
RFX3-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 08, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at