rs61182475
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001314025.2(YBEY):c.210+13T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 1,547,800 control chromosomes in the GnomAD database, including 155,095 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.41 ( 12944 hom., cov: 30)
Exomes 𝑓: 0.44 ( 142151 hom. )
Consequence
YBEY
NM_001314025.2 intron
NM_001314025.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00700
Genes affected
YBEY (HGNC:1299): (ybeY metalloendoribonuclease) This gene encodes a highly conserved metalloprotein. A similar protein in bacteria acts as an endoribonuclease, and is thought to function in ribosomal RNA maturation and ribosome assembly. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 21-46287136-T-A is Benign according to our data. Variant chr21-46287136-T-A is described in ClinVar as [Benign]. Clinvar id is 403614.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YBEY | NM_001314025.2 | c.210+13T>A | intron_variant | ENST00000397701.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YBEY | ENST00000397701.9 | c.210+13T>A | intron_variant | 2 | NM_001314025.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.406 AC: 60977AN: 150198Hom.: 12937 Cov.: 30
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GnomAD3 exomes AF: 0.385 AC: 75237AN: 195262Hom.: 17263 AF XY: 0.383 AC XY: 40910AN XY: 106768
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GnomAD4 exome AF: 0.443 AC: 618785AN: 1397490Hom.: 142151 Cov.: 31 AF XY: 0.439 AC XY: 304665AN XY: 693860
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GnomAD4 genome AF: 0.406 AC: 61002AN: 150310Hom.: 12944 Cov.: 30 AF XY: 0.406 AC XY: 29797AN XY: 73306
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at