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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BACH1	NM_001186.4	MANE Select	c.*331A>G	3_prime_UTR	Exon 5 of 5	NP_001177.1	O14867
BACH1	NM_206866.3		c.*331A>G	3_prime_UTR	Exon 5 of 5	NP_996749.1	O14867
BACH1	NR_027655.3		n.1956-8470A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BACH1	ENST00000286800.8	TSL:1 MANE Select	c.*331A>G	3_prime_UTR	Exon 5 of 5	ENSP00000286800.3	O14867
BACH1	ENST00000399921.5	TSL:1	c.*331A>G	3_prime_UTR	Exon 5 of 5	ENSP00000382805.1	O14867
BACH1	ENST00000888449.1		c.*331A>G	3_prime_UTR	Exon 6 of 6	ENSP00000558508.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over