rs2832332

Positions:

• chr21-29455583-A-G

Variant summary

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

The XR_001754998.2(LOC107985486):​n.82-2397A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 152,276 control chromosomes in the GnomAD database, including 851 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 0.10 (851 hom., cov: 32)
• Consequence: LOC107985486 XR_001754998.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

Genes affected

LOC107985486 (HGNC:):

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 = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985486	XR_001754998.2	n.82-2397A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BACH1	ENST00000422809.5	c.472+125890A>G		intron_variant		5
BACH1	ENST00000468059.1	c.325+125890A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15184 AN: 152158 Hom.: 844 Cov.: 32

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.0998 AC: 15199 AN: 152276 Hom.: 851 Cov.: 32 AF XY: 0.0972 AC XY: 7234 AN XY: 74448

Gnomad4 AFR AF: 0.0753

Gnomad4 AMR AF: 0.0895

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0609

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.119

Alfa AF: 0.116 Hom.: 467

Bravo AF: 0.0991

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2832332; hg19: chr21-30827903;