rs2832283

chr21-29318237-G-A

Variant summary

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

The NM_001186.4(BACH1):c.-60-2984G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,222 control chromosomes in the GnomAD database, including 2,573 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 0.16 (2573 hom., cov: 32)
• Consequence: BACH1 NM_001186.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BACH1	NM_001186.4	c.-60-2984G>A		intron_variant		ENST00000286800.8
BACH1	NM_206866.3	c.-60-2984G>A		intron_variant
BACH1	NR_027655.3	n.120-2984G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BACH1	ENST00000286800.8	c.-60-2984G>A		intron_variant		1	NM_001186.4	P1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24441 AN: 152104 Hom.: 2576 Cov.: 32

Gnomad AFR AF: 0.0387

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.161 AC: 24436 AN: 152222 Hom.: 2573 Cov.: 32 AF XY: 0.163 AC XY: 12147 AN XY: 74422

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.0551

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.173

Alfa AF: 0.208 Hom.: 4777

Bravo AF: 0.142

Asia WGS AF: 0.163 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	13
Dann	Benign	0.77
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2832283; hg19: chr21-30690558;