21-29492828-T-C

Variant names:

• chr21-29492828-T-C
• rs2211887
• ENST00000422809.5:c.472-89484T>C

Variant summary

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

The ENST00000422809.5(BACH1):​c.472-89484T>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 ENST00000422809.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• Publications: 1 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]

LOC105372770 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422809.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BACH1	ENST00000422809.5	TSL:5	c.472-89484T>C		intron	N/A	ENSP00000416569.1
	BACH1	ENST00000468059.1	TSL:3	c.325-104742T>C		intron	N/A	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

African (AFR) AF: 0.504 AC: 20845 AN: 41396

American (AMR) AF: 0.879 AC: 13446 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3339 AN: 3472

East Asian (EAS) AF: 0.842 AC: 4359 AN: 5176

South Asian (SAS) AF: 0.958 AC: 4610 AN: 4814

European-Finnish (FIN) AF: 0.969 AC: 10283 AN: 10614

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66066 AN: 67996

Other (OTH) AF: 0.866 AC: 1827 AN: 2110

Alfa AF: 0.867 Hom.: 7718

Bravo AF: 0.807

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.9
DANN	Benign	0.84
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2211887; hg19: chr21-30865148;