rs4739066
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152758.6(YTHDF3):c.1734+3789A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,152 control chromosomes in the GnomAD database, including 1,463 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 0.12 ( 1463 hom., cov: 32)
Consequence
YTHDF3
NM_152758.6 intron
NM_152758.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.706
Genes affected
YTHDF3 (HGNC:26465): (YTH N6-methyladenosine RNA binding protein F3) This gene encodes a member of the YTH (YT521-B homology) domain protein family. The YTH domain is common in eukaryotes, is often found in the middle of the protein sequence, and may function in binding to RNA. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YTHDF3 | NM_152758.6 | c.1734+3789A>G | intron_variant | ENST00000539294.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YTHDF3 | ENST00000539294.6 | c.1734+3789A>G | intron_variant | 1 | NM_152758.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.121 AC: 18420AN: 152034Hom.: 1460 Cov.: 32
GnomAD3 genomes
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18420
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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: 0.121 AC: 18437AN: 152152Hom.: 1463 Cov.: 32 AF XY: 0.123 AC XY: 9117AN XY: 74398
GnomAD4 genome
?
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18437
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152152
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32
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9117
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74398
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582
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3470
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