NM_001186.4:c.*2583T>C

Variant names:

• chr21-29345416-T-C
• rs372883
• NM_001186.4:c.*2583T>C

Variant summary

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

The NM_001186.4(BACH1):​c.*2583T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,020 control chromosomes in the GnomAD database, including 21,413 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 0.53 (21413 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: BACH1 NM_001186.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 50 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001186.4. 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
	BACH1	NM_001186.4	MANE Select	c.*2583T>C		3_prime_UTR	Exon 5 of 5	NP_001177.1
	BACH1	NM_206866.3		c.*2583T>C		3_prime_UTR	Exon 5 of 5	NP_996749.1
	BACH1	NR_027655.3		n.1956-6218T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BACH1	ENST00000286800.8	TSL:1 MANE Select	c.*2583T>C		3_prime_UTR	Exon 5 of 5	ENSP00000286800.3
	BACH1	ENST00000399921.5	TSL:1	c.*2583T>C		3_prime_UTR	Exon 5 of 5	ENSP00000382805.1
	BACH1	ENST00000422809.5	TSL:5	c.471+15723T>C		intron	N/A	ENSP00000416569.1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79804 AN: 151894 Hom.: 21383 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.527

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 2 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.525 AC: 79873 AN: 152012 Hom.: 21413 Cov.: 33 AF XY: 0.523 AC XY: 38830 AN XY: 74284

African (AFR) AF: 0.614 AC: 25454 AN: 41456

American (AMR) AF: 0.528 AC: 8057 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2404 AN: 5190

South Asian (SAS) AF: 0.629 AC: 3036 AN: 4824

European-Finnish (FIN) AF: 0.429 AC: 4530 AN: 10562

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33096 AN: 67934

Other (OTH) AF: 0.528 AC: 1110 AN: 2104

Alfa AF: 0.500 Hom.: 78101

Bravo AF: 0.533

Asia WGS AF: 0.561 AC: 1945 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.75
PhyloP100		-0.11
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs372883; hg19: chr21-30717737;