5-95656076-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001131066.2(RFESD):c.400C>T(p.Pro134Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000753 in 1,461,280 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 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. P134R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001131066.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RFESD | NM_001131066.2 | c.400C>T | p.Pro134Ser | missense_variant | 6/6 | ENST00000380005.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFESD | ENST00000380005.9 | c.400C>T | p.Pro134Ser | missense_variant | 6/6 | 2 | NM_001131066.2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250604Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135426
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461280Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726960
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2022 | The c.400C>T (p.P134S) alteration is located in exon 6 (coding exon 5) of the RFESD gene. This alteration results from a C to T substitution at nucleotide position 400, causing the proline (P) at amino acid position 134 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