chr4-2512457-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002938.5(RNF4):c.234G>T(p.Arg78Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,612,320 control chromosomes in the GnomAD database, including 1 homozygotes. 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_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.234G>T | p.Arg78Ser | missense_variant | 6/8 | ENST00000314289.13 | |
RNF4 | NM_001185009.3 | c.234G>T | p.Arg78Ser | missense_variant | 7/9 | ||
RNF4 | XM_047416062.1 | c.234G>T | p.Arg78Ser | missense_variant | 7/9 | ||
RNF4 | NM_001185010.3 | c.214+492G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF4 | ENST00000314289.13 | c.234G>T | p.Arg78Ser | missense_variant | 6/8 | 1 | NM_002938.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 246050Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133462
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1460076Hom.: 1 Cov.: 32 AF XY: 0.0000317 AC XY: 23AN XY: 726190
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74432
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.234G>T (p.R78S) alteration is located in exon 7 (coding exon 5) of the RNF4 gene. This alteration results from a G to T substitution at nucleotide position 234, causing the arginine (R) at amino acid position 78 to be replaced by a serine (S). 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