4-68314187-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001031732.4(YTHDC1):c.2096G>A(p.Arg699Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,613,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YTHDC1 | NM_001031732.4 | c.2096G>A | p.Arg699Gln | missense_variant | Exon 17 of 17 | ENST00000344157.9 | NP_001026902.1 | |
YTHDC1 | NM_001330698.2 | c.2120G>A | p.Arg707Gln | missense_variant | Exon 17 of 17 | NP_001317627.1 | ||
YTHDC1 | NM_133370.4 | c.2042G>A | p.Arg681Gln | missense_variant | Exon 16 of 16 | NP_588611.2 | ||
YTHDC1 | XM_005265708.4 | c.2066G>A | p.Arg689Gln | missense_variant | Exon 16 of 16 | XP_005265765.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YTHDC1 | ENST00000344157.9 | c.2096G>A | p.Arg699Gln | missense_variant | Exon 17 of 17 | 1 | NM_001031732.4 | ENSP00000339245.4 | ||
YTHDC1 | ENST00000355665.7 | c.2042G>A | p.Arg681Gln | missense_variant | Exon 16 of 16 | 1 | ENSP00000347888.3 | |||
YTHDC1 | ENST00000579690.5 | c.2120G>A | p.Arg707Gln | missense_variant | Exon 17 of 17 | 5 | ENSP00000463982.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248728Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134568
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461378Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726970
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2096G>A (p.R699Q) alteration is located in exon 17 (coding exon 17) of the YTHDC1 gene. This alteration results from a G to A substitution at nucleotide position 2096, causing the arginine (R) at amino acid position 699 to be replaced by a glutamine (Q). 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