chr5-95654227-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001131066.2(RFESD):c.325C>T(p.Arg109Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,611,710 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R109S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001131066.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RFESD | NM_001131066.2 | c.325C>T | p.Arg109Cys | missense_variant | 4/6 | ENST00000380005.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFESD | ENST00000380005.9 | c.325C>T | p.Arg109Cys | missense_variant | 4/6 | 2 | NM_001131066.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000560 AC: 14AN: 250036Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135132
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1459582Hom.: 0 Cov.: 30 AF XY: 0.0000441 AC XY: 32AN XY: 726114
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.325C>T (p.R109C) alteration is located in exon 4 (coding exon 3) of the RFESD gene. This alteration results from a C to T substitution at nucleotide position 325, causing the arginine (R) at amino acid position 109 to be replaced by a cysteine (C). 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