chr12-101291762-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_014503.3(UTP20):c.912C>T(p.His304=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00778 in 1,599,170 control chromosomes in the GnomAD database, including 136 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 55 hom., cov: 32)
Exomes 𝑓: 0.0067 ( 81 hom. )
Consequence
UTP20
NM_014503.3 synonymous
NM_014503.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.127
Genes affected
UTP20 (HGNC:17897): (UTP20 small subunit processome component) UTP20 is a component of the U3 small nucleolar RNA (snoRNA) (SNORD3A; MIM 180710) protein complex (U3 snoRNP) and is involved in 18S rRNA processing (Wang et al., 2007 [PubMed 17498821]).[supplied by OMIM, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 12-101291762-C-T is Benign according to our data. Variant chr12-101291762-C-T is described in ClinVar as [Benign]. Clinvar id is 782221.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.127 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0184 (2798/152244) while in subpopulation AFR AF= 0.0478 (1983/41526). AF 95% confidence interval is 0.046. There are 55 homozygotes in gnomad4. There are 1335 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 51 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTP20 | NM_014503.3 | c.912C>T | p.His304= | synonymous_variant | 9/62 | ENST00000261637.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTP20 | ENST00000261637.5 | c.912C>T | p.His304= | synonymous_variant | 9/62 | 1 | NM_014503.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0182 AC: 2773AN: 152126Hom.: 51 Cov.: 32
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GnomAD3 exomes AF: 0.00907 AC: 2176AN: 239926Hom.: 21 AF XY: 0.00851 AC XY: 1100AN XY: 129270
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GnomAD4 exome AF: 0.00666 AC: 9640AN: 1446926Hom.: 81 Cov.: 30 AF XY: 0.00655 AC XY: 4708AN XY: 718444
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GnomAD4 genome ? AF: 0.0184 AC: 2798AN: 152244Hom.: 55 Cov.: 32 AF XY: 0.0179 AC XY: 1335AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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