rs873651

chr21-29409528-G-A

Variant summary

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

The ENST00000422809.5(BACH1):c.472+79835G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,082 control chromosomes in the GnomAD database, including 9,341 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 0.31 (9341 hom., cov: 32)
• Consequence: BACH1 ENST00000422809.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 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.472+79835G>A		intron_variant		5
BACH1	ENST00000468059.1	c.325+79835G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47555 AN: 151962 Hom.: 9341 Cov.: 32

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.313 AC: 47550 AN: 152082 Hom.: 9341 Cov.: 32 AF XY: 0.314 AC XY: 23354 AN XY: 74310

Gnomad4 AFR AF: 0.0810

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.333

Alfa AF: 0.354 Hom.: 1800

Bravo AF: 0.294

Asia WGS AF: 0.219 AC: 759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.32
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873651; hg19: chr21-30781848;