21-29492828-T-C

Position:

• chr21-29492828-T-C

Variant summary

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

The ENST00000468059.1(BACH1):​c.325-104742T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,078 control chromosomes in the GnomAD database, including 55,360 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 0.83 (55360 hom., cov: 31)
• Consequence: BACH1 ENST00000468059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.29492828T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BACH1	ENST00000422809.5	c.472-89484T>C		intron_variant		5		ENSP00000416569.1
BACH1	ENST00000468059.1	c.325-104742T>C		intron_variant		3		ENSP00000470673.1

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125928 AN: 151960 Hom.: 55366 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.828 AC: 125950 AN: 152078 Hom.: 55360 Cov.: 31 AF XY: 0.831 AC XY: 61792 AN XY: 74340

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.958

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.866

Alfa AF: 0.883 Hom.: 7622

Bravo AF: 0.807

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.9
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2211887; hg19: chr21-30865148;