4-68318841-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001031732.4(YTHDC1):c.1706A>G(p.Tyr569Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,461,834 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001031732.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YTHDC1 | NM_001031732.4 | c.1706A>G | p.Tyr569Cys | missense_variant | Exon 13 of 17 | ENST00000344157.9 | NP_001026902.1 | |
YTHDC1 | NM_001330698.2 | c.1706A>G | p.Tyr569Cys | missense_variant | Exon 13 of 17 | NP_001317627.1 | ||
YTHDC1 | NM_133370.4 | c.1652A>G | p.Tyr551Cys | missense_variant | Exon 12 of 16 | NP_588611.2 | ||
YTHDC1 | XM_005265708.4 | c.1652A>G | p.Tyr551Cys | missense_variant | Exon 12 of 16 | XP_005265765.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YTHDC1 | ENST00000344157.9 | c.1706A>G | p.Tyr569Cys | missense_variant | Exon 13 of 17 | 1 | NM_001031732.4 | ENSP00000339245.4 | ||
YTHDC1 | ENST00000355665.7 | c.1652A>G | p.Tyr551Cys | missense_variant | Exon 12 of 16 | 1 | ENSP00000347888.3 | |||
YTHDC1 | ENST00000579690.5 | c.1706A>G | p.Tyr569Cys | missense_variant | Exon 13 of 17 | 5 | ENSP00000463982.1 | |||
YTHDC1 | ENST00000507529.1 | c.-122A>G | upstream_gene_variant | 3 | ENSP00000461990.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251184Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135766
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461834Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727216
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1706A>G (p.Y569C) alteration is located in exon 13 (coding exon 13) of the YTHDC1 gene. This alteration results from a A to G substitution at nucleotide position 1706, causing the tyrosine (Y) at amino acid position 569 to be replaced by a cysteine (C). 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