21-29518574-A-G

Position:

• chr21-29518574-A-G

Variant summary

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

The ENST00000422809.5(BACH1):​c.473-63738A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,084 control chromosomes in the GnomAD database, including 26,724 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 0.55 (26724 hom., cov: 32)
• Consequence: BACH1 ENST00000422809.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

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=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BACH1	ENST00000422809.5	c.473-63738A>G		intron_variant		5		ENSP00000416569
BACH1	ENST00000468059.1	c.326-78996A>G		intron_variant		3		ENSP00000470673

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83712 AN: 151966 Hom.: 26720 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.551 AC: 83725 AN: 152084 Hom.: 26724 Cov.: 32 AF XY: 0.552 AC XY: 41040 AN XY: 74344

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.574

Alfa AF: 0.681 Hom.: 47225

Bravo AF: 0.524

Asia WGS AF: 0.544 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2832387; hg19: chr21-30890894;