5-71458756-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_018429.3(BDP1):c.390C>T(p.Ala130=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
BDP1
NM_018429.3 synonymous
NM_018429.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.66
Genes affected
BDP1 (HGNC:13652): (B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB) The product of this gene is a subunit of the TFIIIB transcription initiation complex, which recruits RNA polymerase III to target promoters in order to initiate transcription. The encoded protein localizes to concentrated aggregates in the nucleus, and is required for transcription from all three types of polymerase III promoters. It is phosphorylated by casein kinase II during mitosis, resulting in its release from chromatin and suppression of polymerase III transcription. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 5-71458756-C-T is Benign according to our data. Variant chr5-71458756-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1318315.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.66 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BDP1 | NM_018429.3 | c.390C>T | p.Ala130= | synonymous_variant | 2/39 | ENST00000358731.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BDP1 | ENST00000358731.9 | c.390C>T | p.Ala130= | synonymous_variant | 2/39 | 1 | NM_018429.3 | P1 | |
BDP1 | ENST00000508917.6 | n.582C>T | non_coding_transcript_exon_variant | 2/32 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249488Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135354
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GnomAD4 exome AF: 0.000122 AC: 179AN: 1461778Hom.: 0 Cov.: 32 AF XY: 0.000116 AC XY: 84AN XY: 727196
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74328
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 17, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at