rs2832332

Variant names:

• chr21-29455583-A-G
• rs2832332
• ENST00000422809.5:c.471+125890A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000468059.1(BACH1):​c.324+125890A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 152,276 control chromosomes in the GnomAD database, including 851 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 0.10 (851 hom., cov: 32)
• Consequence: BACH1 ENST00000468059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 1 publications found

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]

LOC107985486 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000468059.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BACH1	ENST00000422809.5	TSL:5	c.471+125890A>G		intron	N/A	ENSP00000416569.1	H7C4B6
	BACH1	ENST00000468059.1	TSL:3	c.324+125890A>G		intron	N/A	ENSP00000470673.1	M0QZP0

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15184 AN: 152158 Hom.: 844 Cov.: 32

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.0998 AC: 15199 AN: 152276 Hom.: 851 Cov.: 32 AF XY: 0.0972 AC XY: 7234 AN XY: 74448

African (AFR) AF: 0.0753 AC: 3131 AN: 41572

American (AMR) AF: 0.0895 AC: 1368 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5184

South Asian (SAS) AF: 0.0609 AC: 294 AN: 4828

European-Finnish (FIN) AF: 0.0891 AC: 946 AN: 10616

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8672 AN: 68004

Other (OTH) AF: 0.119 AC: 250 AN: 2108

Alfa AF: 0.113 Hom.: 704

Bravo AF: 0.0991

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.81
PhyloP100		-0.018

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2832332;

hg19: chr21-30827903;