chr5-113513930-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_022828.5(YTHDC2):c.35C>T(p.Pro12Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 1,605,508 control chromosomes in the GnomAD database, including 18 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_022828.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YTHDC2 | NM_022828.5 | c.35C>T | p.Pro12Leu | missense_variant | 1/30 | ENST00000161863.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YTHDC2 | ENST00000161863.9 | c.35C>T | p.Pro12Leu | missense_variant | 1/30 | 1 | NM_022828.5 | P1 | |
YTHDC2 | ENST00000515883.5 | c.35C>T | p.Pro12Leu | missense_variant | 1/17 | 1 | |||
YTHDC2 | ENST00000503857.5 | c.35C>T | p.Pro12Leu | missense_variant, NMD_transcript_variant | 1/16 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00648 AC: 987AN: 152226Hom.: 7 Cov.: 33
GnomAD3 exomes AF: 0.00149 AC: 341AN: 228386Hom.: 3 AF XY: 0.00113 AC XY: 142AN XY: 125912
GnomAD4 exome AF: 0.000617 AC: 896AN: 1453168Hom.: 11 Cov.: 31 AF XY: 0.000530 AC XY: 383AN XY: 722076
GnomAD4 genome AF: 0.00648 AC: 987AN: 152340Hom.: 7 Cov.: 33 AF XY: 0.00628 AC XY: 468AN XY: 74488
ClinVar
Submissions by phenotype
YTHDC2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at