4-2497067-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002938.5(RNF4):āc.70A>Cā(p.Thr24Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002938.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF4 | NM_002938.5 | c.70A>C | p.Thr24Pro | missense_variant | 3/8 | ENST00000314289.13 | |
RNF4 | NM_001185009.3 | c.70A>C | p.Thr24Pro | missense_variant | 4/9 | ||
RNF4 | NM_001185010.3 | c.70A>C | p.Thr24Pro | missense_variant | 3/7 | ||
RNF4 | XM_047416062.1 | c.70A>C | p.Thr24Pro | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF4 | ENST00000314289.13 | c.70A>C | p.Thr24Pro | missense_variant | 3/8 | 1 | NM_002938.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151766Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151766Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74096
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 04, 2023 | The c.70A>C (p.T24P) alteration is located in exon 4 (coding exon 2) of the RNF4 gene. This alteration results from a A to C substitution at nucleotide position 70, causing the threonine (T) at amino acid position 24 to be replaced by a proline (P). 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