9-3247951-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_002919.4(RFX3):c.2049G>A(p.Leu683Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.013 in 1,613,454 control chromosomes in the GnomAD database, including 2,020 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_002919.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RFX3 | ENST00000358730.6 | c.2049G>A | p.Leu683Leu | synonymous_variant | Exon 14 of 14 | 1 | ENSP00000351574.2 | |||
RFX3 | ENST00000617270.5 | c.1968+81G>A | intron_variant | Intron 15 of 16 | 2 | NM_001282116.2 | ENSP00000482598.1 | |||
RFX3 | ENST00000382004.7 | c.1968+81G>A | intron_variant | Intron 16 of 17 | 1 | ENSP00000371434.3 | ||||
RFX3 | ENST00000449234.1 | c.363+81G>A | intron_variant | Intron 2 of 2 | 3 | ENSP00000415594.1 |
Frequencies
GnomAD3 genomes AF: 0.0660 AC: 10037AN: 152044Hom.: 1104 Cov.: 32
GnomAD3 exomes AF: 0.0185 AC: 4628AN: 250110Hom.: 446 AF XY: 0.0142 AC XY: 1918AN XY: 135282
GnomAD4 exome AF: 0.00745 AC: 10891AN: 1461290Hom.: 912 Cov.: 33 AF XY: 0.00663 AC XY: 4817AN XY: 726990
GnomAD4 genome AF: 0.0661 AC: 10059AN: 152164Hom.: 1108 Cov.: 32 AF XY: 0.0638 AC XY: 4745AN XY: 74408
ClinVar
Submissions by phenotype
RFX3-related disorder Benign:1
This variant is classified as 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