rs1730874
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001031732.4(YTHDC1):c.1825-535C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 152,332 control chromosomes in the GnomAD database, including 75,291 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.99 ( 75291 hom., cov: 32)
Consequence
YTHDC1
NM_001031732.4 intron
NM_001031732.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.383
Genes affected
YTHDC1 (HGNC:30626): (YTH N6-methyladenosine RNA binding protein C1) Enables N6-methyladenosine-containing RNA binding activity. Involved in mRNA export from nucleus; mRNA splice site selection; and regulation of gene expression. Located in nuclear speck and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YTHDC1 | NM_001031732.4 | c.1825-535C>T | intron_variant | ENST00000344157.9 | |||
YTHDC1 | NM_001330698.2 | c.1849-535C>T | intron_variant | ||||
YTHDC1 | NM_133370.4 | c.1771-535C>T | intron_variant | ||||
YTHDC1 | XM_005265708.4 | c.1795-535C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YTHDC1 | ENST00000344157.9 | c.1825-535C>T | intron_variant | 1 | NM_001031732.4 | P2 | |||
YTHDC1 | ENST00000355665.7 | c.1771-535C>T | intron_variant | 1 | A2 | ||||
YTHDC1 | ENST00000507529.1 | c.96-535C>T | intron_variant | 3 | |||||
YTHDC1 | ENST00000579690.5 | c.1849-535C>T | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.994 AC: 151331AN: 152214Hom.: 75233 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.994 AC: 151448AN: 152332Hom.: 75291 Cov.: 32 AF XY: 0.995 AC XY: 74085AN XY: 74492
GnomAD4 genome
?
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151448
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32
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74085
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74492
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3475
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at