rs2832337

chr21-29460151-T-C

Variant summary

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

The XR_001754998.2(LOC107985486):n.2253T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,144 control chromosomes in the GnomAD database, including 3,682 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 0.19 (3682 hom., cov: 32)
• Consequence: LOC107985486 XR_001754998.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985486	XR_001754998.2	n.2253T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BACH1	ENST00000422809.5	c.473-122161T>C		intron_variant		5
BACH1	ENST00000468059.1	c.325+130458T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28143 AN: 152026 Hom.: 3656 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0456

Gnomad SAS AF: 0.0627

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.185 AC: 28210 AN: 152144 Hom.: 3682 Cov.: 32 AF XY: 0.180 AC XY: 13361 AN XY: 74390

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0455

Gnomad4 SAS AF: 0.0626

Gnomad4 FIN AF: 0.0893

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.177

Alfa AF: 0.141 Hom.: 2542

Bravo AF: 0.197

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.9
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2832337; hg19: chr21-30832471;