rs2832357

chr21-29491574-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422809.5(BACH1):c.473-90738A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,174 control chromosomes in the GnomAD database, including 2,226 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (2226 hom., cov: 33)
• Consequence: BACH1 ENST00000422809.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BACH1	ENST00000422809.5	c.473-90738A>G		intron_variant		5
BACH1	ENST00000468059.1	c.326-105996A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17807 AN: 152056 Hom.: 2209 Cov.: 33

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0311

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0279

Gnomad OTH AF: 0.0930

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.118 AC: 17885 AN: 152174 Hom.: 2226 Cov.: 33 AF XY: 0.117 AC XY: 8704 AN XY: 74402

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0283

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.0311

Gnomad4 NFE AF: 0.0279

Gnomad4 OTH AF: 0.0963

Alfa AF: 0.0541 Hom.: 280

Bravo AF: 0.132

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	3.7
Dann	Benign	0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2832357; hg19: chr21-30863894;