12-106687017-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_213594.3(RFX4):c.511C>T(p.Arg171Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000744 in 1,613,862 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R171Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_213594.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RFX4 | NM_213594.3 | c.511C>T | p.Arg171Trp | missense_variant | Exon 6 of 18 | ENST00000392842.6 | NP_998759.1 | |
RFX4 | NM_001206691.2 | c.538C>T | p.Arg180Trp | missense_variant | Exon 6 of 18 | NP_001193620.1 | ||
RFX4 | NM_032491.6 | c.229C>T | p.Arg77Trp | missense_variant | Exon 2 of 14 | NP_115880.2 | ||
LOC100287944 | NR_040246.1 | n.142+87673G>A | intron_variant | Intron 1 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151978Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251484Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461884Hom.: 0 Cov.: 35 AF XY: 0.0000110 AC XY: 8AN XY: 727240
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151978Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.538C>T (p.R180W) alteration is located in exon 6 (coding exon 6) of the RFX4 gene. This alteration results from a C to T substitution at nucleotide position 538, causing the arginine (R) at amino acid position 180 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