chr1-207050976-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018566.4(YOD1):c.55C>T(p.Pro19Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000214 in 1,541,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign 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. P19L) has been classified as Uncertain significance.
Frequency
Consequence
NM_018566.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YOD1 | NM_018566.4 | c.55C>T | p.Pro19Ser | missense_variant | 1/2 | ENST00000315927.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YOD1 | ENST00000315927.9 | c.55C>T | p.Pro19Ser | missense_variant | 1/2 | 1 | NM_018566.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152268Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 18AN: 151052Hom.: 0 AF XY: 0.000109 AC XY: 9AN XY: 82932
GnomAD4 exome AF: 0.0000180 AC: 25AN: 1389442Hom.: 0 Cov.: 31 AF XY: 0.0000146 AC XY: 10AN XY: 683660
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152386Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74520
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2023 | The c.55C>T (p.P19S) alteration is located in exon 1 (coding exon 1) of the YOD1 gene. This alteration results from a C to T substitution at nucleotide position 55, causing the proline (P) at amino acid position 19 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