rs2832337

Variant names:

• chr21-29460151-T-C
• rs2832337
• ENST00000422809.5:c.472-122161T>C

Variant summary

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

The ENST00000468059.1(BACH1):​c.324+130458T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,144 control chromosomes in the GnomAD database, including 3,682 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 0.19 (3682 hom., cov: 32)
• Consequence: BACH1 ENST00000468059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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.472-122161T>C		intron	N/A	ENSP00000416569.1	H7C4B6
	BACH1	ENST00000468059.1	TSL:3	c.324+130458T>C		intron	N/A	ENSP00000470673.1	M0QZP0
	ENSG00000296905	ENST00000743445.1		n.123-99T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28143 AN: 152026 Hom.: 3656 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0456

Gnomad SAS AF: 0.0627

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.185 AC: 28210 AN: 152144 Hom.: 3682 Cov.: 32 AF XY: 0.180 AC XY: 13361 AN XY: 74390

African (AFR) AF: 0.367 AC: 15222 AN: 41458

American (AMR) AF: 0.119 AC: 1825 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3466

East Asian (EAS) AF: 0.0455 AC: 236 AN: 5188

South Asian (SAS) AF: 0.0626 AC: 302 AN: 4826

European-Finnish (FIN) AF: 0.0893 AC: 946 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8739 AN: 67992

Other (OTH) AF: 0.177 AC: 374 AN: 2114

Alfa AF: 0.148 Hom.: 3944

Bravo AF: 0.197

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		-0.76

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: rs2832337;

hg19: chr21-30832471;