Genetic Variant BACH1:c.*2583T>C (chr21-29345416-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.108

Publications

50 publications found

Variant links:

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]

BACH1 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
BACH1	NM_001186.4 link	c.*2583T>C	3_prime_UTR_variant	Exon 5 of 5	ENST00000286800.8	NP_001177.1
BACH1	NM_206866.3 link	c.*2583T>C	3_prime_UTR_variant	Exon 5 of 5		NP_996749.1
BACH1	NR_027655.3 link	n.1956-6218T>C	intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
BACH1	ENST00000286800.8 link	c.*2583T>C	3_prime_UTR_variant	Exon 5 of 5	1	NM_001186.4	ENSP00000286800.3
BACH1	ENST00000399921.5 link	c.*2583T>C	3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000382805.1
BACH1	ENST00000422809.5 link	c.471+15723T>C	intron_variant	Intron 2 of 4	5		ENSP00000416569.1
BACH1	ENST00000468059.1 link	c.324+15723T>C	intron_variant	Intron 2 of 3	3		ENSP00000470673.1

Frequencies

GnomAD3 genomes

AF:

0.525

AC:

79804

AN:

151894

Hom.:

21383

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.600

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.525

AC:

79873

AN:

152012

Hom.:

21413

Cov.:

AF XY:

0.523

AC XY:

38830

AN XY:

74284

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1967

3934

5900

7867

9834

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

702

1404

2106

2808

3510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.2

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over