rs388707
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The ENST00000286800.8(BACH1):āc.1833T>Cā(p.Gly611=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,613,806 control chromosomes in the GnomAD database, including 161,378 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: š 0.49 ( 19501 hom., cov: 33)
Exomes š: 0.44 ( 141877 hom. )
Consequence
BACH1
ENST00000286800.8 synonymous
ENST00000286800.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.61
Genes affected
BACH1 (HGNC:935): (BTB domain and CNC homolog 1) This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 21-29342455-T-C is Benign according to our data. Variant chr21-29342455-T-C is described in ClinVar as [Benign]. Clinvar id is 3059943.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-2.61 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BACH1 | NM_001186.4 | c.1833T>C | p.Gly611= | synonymous_variant | 5/5 | ENST00000286800.8 | NP_001177.1 | |
BACH1 | NM_206866.3 | c.1833T>C | p.Gly611= | synonymous_variant | 5/5 | NP_996749.1 | ||
BACH1 | NR_027655.3 | n.1956-9179T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BACH1 | ENST00000286800.8 | c.1833T>C | p.Gly611= | synonymous_variant | 5/5 | 1 | NM_001186.4 | ENSP00000286800 | P1 | |
BACH1 | ENST00000399921.5 | c.1833T>C | p.Gly611= | synonymous_variant | 5/5 | 1 | ENSP00000382805 | P1 | ||
BACH1 | ENST00000422809.5 | c.472+12762T>C | intron_variant | 5 | ENSP00000416569 | |||||
BACH1 | ENST00000468059.1 | c.325+12762T>C | intron_variant | 3 | ENSP00000470673 |
Frequencies
GnomAD3 genomes AF: 0.494 AC: 75020AN: 151886Hom.: 19476 Cov.: 33
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GnomAD3 exomes AF: 0.470 AC: 117996AN: 251236Hom.: 28777 AF XY: 0.468 AC XY: 63591AN XY: 135786
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GnomAD4 exome AF: 0.436 AC: 637340AN: 1461802Hom.: 141877 Cov.: 59 AF XY: 0.439 AC XY: 319247AN XY: 727204
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GnomAD4 genome AF: 0.494 AC: 75090AN: 152004Hom.: 19501 Cov.: 33 AF XY: 0.492 AC XY: 36567AN XY: 74290
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
BACH1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 16, 2019 | This variant is classified as 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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at