1-91979679-T-C
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_207189.4(BRDT):āc.1209T>Cā(p.Asn403=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,614,074 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 (ā ).
Frequency
Genomes: š 0.00013 ( 0 hom., cov: 31)
Exomes š: 0.000068 ( 0 hom. )
Consequence
BRDT
NM_207189.4 synonymous
NM_207189.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.32
Genes affected
BRDT (HGNC:1105): (bromodomain testis associated) BRDT is similar to the RING3 protein family. It possesses 2 bromodomain motifs and a PEST sequence (a cluster of proline, glutamic acid, serine, and threonine residues), characteristic of proteins that undergo rapid intracellular degradation. The bromodomain is found in proteins that regulate transcription. Several transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Jun 2011]
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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=-0.53).
BP6
Variant 1-91979679-T-C is Benign according to our data. Variant chr1-91979679-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3037564.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.32 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRDT | NM_207189.4 | c.1209T>C | p.Asn403= | synonymous_variant | 8/19 | ENST00000399546.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRDT | ENST00000399546.7 | c.1209T>C | p.Asn403= | synonymous_variant | 8/19 | 2 | NM_207189.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152176Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000330 AC: 83AN: 251334Hom.: 0 AF XY: 0.000294 AC XY: 40AN XY: 135856
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GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461780Hom.: 0 Cov.: 30 AF XY: 0.0000605 AC XY: 44AN XY: 727192
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GnomAD4 genome AF: 0.000131 AC: 20AN: 152294Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74470
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
BRDT-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 27, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at