chr20-3934069-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001134337.3(RNF24):c.441T>G(p.Ile147Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000668 in 1,495,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001134337.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF24 | NM_001134337.3 | c.441T>G | p.Ile147Met | missense_variant | 6/6 | ENST00000358395.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF24 | ENST00000358395.11 | c.441T>G | p.Ile147Met | missense_variant | 6/6 | 1 | NM_001134337.3 | P1 | |
RNF24 | ENST00000545616.2 | c.504T>G | p.Ile168Met | missense_variant | 7/7 | 1 | |||
RNF24 | ENST00000336095.10 | c.441T>G | p.Ile147Met | missense_variant | 6/6 | 1 | P1 | ||
RNF24 | ENST00000432261.6 | c.504T>G | p.Ile168Met | missense_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152048Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000130 AC: 2AN: 154164Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82726
GnomAD4 exome AF: 0.00000521 AC: 7AN: 1343842Hom.: 0 Cov.: 30 AF XY: 0.00000454 AC XY: 3AN XY: 661156
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152048Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 30, 2023 | The c.504T>G (p.I168M) alteration is located in exon 7 (coding exon 6) of the RNF24 gene. This alteration results from a T to G substitution at nucleotide position 504, causing the isoleucine (I) at amino acid position 168 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