rs8135758
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013313.5(YPEL1):c.-164-11208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,160 control chromosomes in the GnomAD database, including 1,692 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 0.13 ( 1692 hom., cov: 32)
Consequence
YPEL1
NM_013313.5 intron
NM_013313.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.460
Genes affected
YPEL1 (HGNC:12845): (yippee like 1) This gene is located in the region associated with DiGeorge syndrome on chromosome 22. The encoded protein localizes to the centrosome and nucleolus and may play a role in the regulation of cell division. [provided by RefSeq, Feb 2015]
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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=-0.71).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YPEL1 | NM_013313.5 | c.-164-11208C>T | intron_variant | ENST00000339468.8 | |||
YPEL1 | XM_047441355.1 | c.-165+1285C>T | intron_variant | ||||
YPEL1 | NR_130910.2 | n.181-11208C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YPEL1 | ENST00000339468.8 | c.-164-11208C>T | intron_variant | 1 | NM_013313.5 | P1 | |||
YPEL1 | ENST00000403503.1 | c.-164-11208C>T | intron_variant | 3 | |||||
YPEL1 | ENST00000477675.1 | n.148-11208C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.133 AC: 20254AN: 152042Hom.: 1692 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: 0.133 AC: 20260AN: 152160Hom.: 1692 Cov.: 32 AF XY: 0.132 AC XY: 9816AN XY: 74386
GnomAD4 genome
?
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20260
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152160
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32
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9816
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74386
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182
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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