Genetic Variant NM_001186.4:c.*331A>G (chr21-29343164-A-G) – 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.*331A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0265 in 175,630 control chromosomes in the GnomAD database, including 234 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 0.027 ( 197 hom., cov: 32)

Exomes 𝑓: 0.020 ( 37 hom. )

Consequence

BACH1
NM_001186.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65

Publications

12 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BACH1	NM_001186.4 link	c.*331A>G	3_prime_UTR_variant	Exon 5 of 5	ENST00000286800.8	NP_001177.1	O14867
BACH1	NM_206866.3 link	c.*331A>G	3_prime_UTR_variant	Exon 5 of 5		NP_996749.1	O14867
BACH1	NR_027655.3 link	n.1956-8470A>G	intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BACH1	ENST00000286800.8 link	c.*331A>G	3_prime_UTR_variant	Exon 5 of 5	1	NM_001186.4	ENSP00000286800.3	O14867
BACH1	ENST00000399921.5 link	c.*331A>G	3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000382805.1	O14867
BACH1	ENST00000422809.5 link	c.471+13471A>G	intron_variant	Intron 2 of 4	5		ENSP00000416569.1	H7C4B6
BACH1	ENST00000468059.1 link	c.324+13471A>G	intron_variant	Intron 2 of 3	3		ENSP00000470673.1	M0QZP0

Frequencies

GnomAD3 genomes

AF:

0.0274

AC:

4164

AN:

152222

Hom.:

197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0597

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0268

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.00807

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00156

Gnomad OTH

AF:

0.0206

GnomAD4 exome

AF:

0.0201

AC:

468

AN:

23290

Hom.:

Cov.:

AF XY:

0.0190

AC XY:

230

AN XY:

12082

show subpopulations

African (AFR)

AF:

0.0647

AC:

AN:

742

American (AMR)

AF:

0.0393

AC:

107

AN:

2726

Ashkenazi Jewish (ASJ)

AF:

0.00147

AC:

AN:

680

East Asian (EAS)

AF:

0.187

AC:

265

AN:

1414

South Asian (SAS)

AF:

0.00305

AC:

AN:

1638

European-Finnish (FIN)

AF:

0.00

AC:

AN:

722

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00128

AC:

AN:

14080

Other (OTH)

AF:

0.0198

AC:

AN:

1212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0275

AC:

4183

AN:

152340

Hom.:

197

Cov.:

AF XY:

0.0283

AC XY:

2108

AN XY:

74500

show subpopulations

African (AFR)

AF:

0.0599

AC:

2490

AN:

41566

American (AMR)

AF:

0.0271

AC:

415

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.209

AC:

1085

AN:

5182

South Asian (SAS)

AF:

0.00828

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.000188

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00156

AC:

106

AN:

68044

Other (OTH)

AF:

0.0203

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

196

391

587

782

978

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<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:

0.0125

Hom.:

178

Bravo

AF:

0.0337

Asia WGS

AF:

0.0730

AC:

254

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.16

(source)

DANN

Benign

0.75

PhyloP100

-1.6

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over