9-101540295-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_019592.7(RNF20):āc.222G>Cā(p.Glu74Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000805 in 1,614,034 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_019592.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF20 | NM_019592.7 | c.222G>C | p.Glu74Asp | missense_variant | 3/20 | ENST00000389120.8 | |
RNF20 | XM_011518862.2 | c.222G>C | p.Glu74Asp | missense_variant | 3/20 | ||
RNF20 | XM_047423594.1 | c.222G>C | p.Glu74Asp | missense_variant | 4/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF20 | ENST00000389120.8 | c.222G>C | p.Glu74Asp | missense_variant | 3/20 | 1 | NM_019592.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251480Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135916
GnomAD4 exome AF: 0.0000855 AC: 125AN: 1461878Hom.: 1 Cov.: 32 AF XY: 0.0000921 AC XY: 67AN XY: 727246
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.222G>C (p.E74D) alteration is located in exon 3 (coding exon 2) of the RNF20 gene. This alteration results from a G to C substitution at nucleotide position 222, causing the glutamic acid (E) at amino acid position 74 to be replaced by an aspartic acid (D). 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