chr14-73491111-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024644.5(RIOX1):c.94C>A(p.Leu32Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00306 in 1,606,864 control chromosomes in the GnomAD database, including 110 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_024644.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RIOX1 | ENST00000304061.8 | c.94C>A | p.Leu32Met | missense_variant | Exon 1 of 1 | 6 | NM_024644.5 | ENSP00000477507.1 | ||
HEATR4 | ENST00000553558.6 | c.2844+1955G>T | intron_variant | Intron 17 of 17 | 2 | NM_001220484.1 | ENSP00000450444.2 | |||
HEATR4 | ENST00000334988.2 | c.2844+1955G>T | intron_variant | Intron 16 of 16 | 1 | ENSP00000335447.2 | ||||
HEATR4 | ENST00000565094.1 | n.25+645G>T | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0135 AC: 2049AN: 152230Hom.: 44 Cov.: 33
GnomAD3 exomes AF: 0.00400 AC: 958AN: 239778Hom.: 10 AF XY: 0.00328 AC XY: 429AN XY: 130800
GnomAD4 exome AF: 0.00197 AC: 2865AN: 1454516Hom.: 65 Cov.: 84 AF XY: 0.00177 AC XY: 1283AN XY: 723376
GnomAD4 genome AF: 0.0135 AC: 2055AN: 152348Hom.: 45 Cov.: 33 AF XY: 0.0133 AC XY: 988AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at