5-71564883-T-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_018429.3(BDP1):āc.7873T>Gā(p.Ter2625GluextTer11) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000625 in 1,583,314 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.00056 ( 0 hom., cov: 33)
Exomes š: 0.00063 ( 3 hom. )
Consequence
BDP1
NM_018429.3 stop_lost
NM_018429.3 stop_lost
Scores
1
2
4
Clinical Significance
Conservation
PhyloP100: 2.62
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 -2 ACMG points.
PM4
Stoplost variant in NM_018429.3 Downstream stopcodon found after 2699 codons.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BDP1 | NM_018429.3 | c.7873T>G | p.Ter2625GluextTer11 | stop_lost | 39/39 | ENST00000358731.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BDP1 | ENST00000358731.9 | c.7873T>G | p.Ter2625GluextTer11 | stop_lost | 39/39 | 1 | NM_018429.3 | P1 | |
BDP1 | ENST00000525844.1 | c.*239T>G | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | 1 | ||||
BDP1 | ENST00000514903.7 | c.*823T>G | 3_prime_UTR_variant, NMD_transcript_variant | 16/16 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000558 AC: 85AN: 152200Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000872 AC: 196AN: 224672Hom.: 1 AF XY: 0.000962 AC XY: 118AN XY: 122698
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GnomAD4 exome AF: 0.000632 AC: 905AN: 1430996Hom.: 3 Cov.: 30 AF XY: 0.000671 AC XY: 477AN XY: 711394
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GnomAD4 genome AF: 0.000558 AC: 85AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000591 AC XY: 44AN XY: 74460
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:2Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Hearing loss, autosomal recessive 112 Pathogenic:2Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 26, 2024 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 30, 2019 | - - |
Pathogenic, criteria provided, single submitter | research | Laboratory of Prof. Karen Avraham, Tel Aviv University | Apr 18, 2024 | Likely pathogenic by Deafness Variation Database and pathogenic according to PMID: 24312468 - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 05, 2021 | This variant is associated with the following publications: (PMID: 27884173, 24312468, 25060281) - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
D;N
Vest4
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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