chr2-112550939-T-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_019014.6(POLR1B):c.699T>A(p.Thr233=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 1,612,808 control chromosomes in the GnomAD database, including 392,015 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.64 ( 31984 hom., cov: 32)
Exomes 𝑓: 0.70 ( 360031 hom. )
Consequence
POLR1B
NM_019014.6 synonymous
NM_019014.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.92
Genes affected
POLR1B (HGNC:20454): (RNA polymerase I subunit B) Eukaryotic RNA polymerase I (pol I) is responsible for the transcription of ribosomal RNA (rRNA) genes and production of rRNA, the primary component of ribosomes. Pol I is a multisubunit enzyme composed of 6 to 14 polypeptides, depending on the species. Most of the mass of the pol I complex derives from the 2 largest subunits, Rpa1 and Rpa2 in yeast. POLR1B is homologous to Rpa2 (Seither and Grummt, 1996 [PubMed 8921381]).[supplied by OMIM, Mar 2008]
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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=-0.66).
BP6
?
Variant 2-112550939-T-A is Benign according to our data. Variant chr2-112550939-T-A is described in ClinVar as [Benign]. Clinvar id is 1178754.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.92 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLR1B | NM_019014.6 | c.699T>A | p.Thr233= | synonymous_variant | 5/15 | ENST00000263331.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLR1B | ENST00000263331.10 | c.699T>A | p.Thr233= | synonymous_variant | 5/15 | 2 | NM_019014.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.641 AC: 97347AN: 151940Hom.: 31974 Cov.: 32
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GnomAD3 exomes AF: 0.644 AC: 161896AN: 251426Hom.: 53934 AF XY: 0.655 AC XY: 89043AN XY: 135886
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GnomAD4 exome AF: 0.697 AC: 1018421AN: 1460750Hom.: 360031 Cov.: 45 AF XY: 0.698 AC XY: 507593AN XY: 726750
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GnomAD4 genome ? AF: 0.641 AC: 97395AN: 152058Hom.: 31984 Cov.: 32 AF XY: 0.634 AC XY: 47115AN XY: 74326
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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 | GeneDx | May 04, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at