1-37807880-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024640.4(YRDC):āc.301G>Cā(p.Ala101Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000123 in 1,458,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024640.4 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 |
---|---|---|---|---|---|---|---|
YRDC | NM_024640.4 | c.301G>C | p.Ala101Pro | missense_variant | 1/5 | ENST00000373044.3 | |
C1orf122 | NM_198446.3 | c.-525C>G | 5_prime_UTR_variant | 1/3 | ENST00000373042.5 | ||
C1orf122 | NM_001142726.2 | c.-581C>G | 5_prime_UTR_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YRDC | ENST00000373044.3 | c.301G>C | p.Ala101Pro | missense_variant | 1/5 | 1 | NM_024640.4 | P1 | |
C1orf122 | ENST00000373042.5 | c.-525C>G | 5_prime_UTR_variant | 1/3 | 1 | NM_198446.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152114Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000842 AC: 11AN: 1306764Hom.: 0 Cov.: 31 AF XY: 0.00000778 AC XY: 5AN XY: 642374
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74310
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 22, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with YRDC-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.03%). This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 101 of the YRDC protein (p.Ala101Pro). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at