chr1-37807972-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_024640.4(YRDC):āc.209T>Cā(p.Leu70Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000056 in 1,213,786 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. L70L) has been classified as Likely benign.
Frequency
Consequence
NM_024640.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YRDC | NM_024640.4 | c.209T>C | p.Leu70Pro | missense_variant | 1/5 | ENST00000373044.3 | |
C1orf122 | NM_198446.3 | c.-433A>G | 5_prime_UTR_variant | 1/3 | ENST00000373042.5 | ||
C1orf122 | NM_001142726.2 | c.-489A>G | 5_prime_UTR_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YRDC | ENST00000373044.3 | c.209T>C | p.Leu70Pro | missense_variant | 1/5 | 1 | NM_024640.4 | P1 | |
C1orf122 | ENST00000373042.5 | c.-433A>G | 5_prime_UTR_variant | 1/3 | 1 | NM_198446.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000400 AC: 6AN: 150082Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000583 AC: 62AN: 1063704Hom.: 0 Cov.: 30 AF XY: 0.0000438 AC XY: 22AN XY: 502814
GnomAD4 genome AF: 0.0000400 AC: 6AN: 150082Hom.: 0 Cov.: 33 AF XY: 0.0000683 AC XY: 5AN XY: 73234
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.209T>C (p.L70P) alteration is located in exon 1 (coding exon 1) of the YRDC gene. This alteration results from a T to C substitution at nucleotide position 209, causing the leucine (L) at amino acid position 70 to be replaced by a proline (P). 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