Genetic Variant BACH2:c.*3164C>T (chr6-89929244-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_021813.4(BACH2):c.*3164C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,294 control chromosomes in the GnomAD database, including 1,848 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 0.15 ( 1846 hom., cov: 32)

Exomes 𝑓: 0.17 ( 2 hom. )

Consequence

BACH2
NM_021813.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.507

Publications

13 publications found

Variant links:

Genes affected

BACH2 (HGNC:14078): (BTB domain and CNC homolog 2) Enables sequence-specific double-stranded DNA binding activity. Involved in primary adaptive immune response involving T cells and B cells. Located in cytosol and nucleoplasm. Implicated in immunodeficiency 60. [provided by Alliance of Genome Resources, Apr 2022]

BACH2 Gene-Disease associations (from GenCC):

immunodeficiency 60
Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Illumina, ClinGen, Ambry Genetics

BACH2 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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021813.4. 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
	BACH2	NM_021813.4	MANE Select	c.*3164C>T		3_prime_UTR	Exon 9 of 9	NP_068585.1
	BACH2	NM_001170794.2		c.*3164C>T		3_prime_UTR	Exon 7 of 7	NP_001164265.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BACH2	ENST00000257749.9	TSL:1 MANE Select	c.*3164C>T		3_prime_UTR	Exon 9 of 9	ENSP00000257749.4

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22207

AN:

152018

Hom.:

1844

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0894

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.252

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.171

AC:

AN:

158

Hom.:

Cov.:

AF XY:

0.178

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.174

AC:

AN:

138

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.214

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.445

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

<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:

0.146

AC:

22220

AN:

152136

Hom.:

1846

Cov.:

AF XY:

0.146

AC XY:

10887

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.0895

AC:

3716

AN:

41502

American (AMR)

AF:

0.178

AC:

2718

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.238

AC:

827

AN:

3468

East Asian (EAS)

AF:

0.206

AC:

1065

AN:

5164

South Asian (SAS)

AF:

0.255

AC:

1230

AN:

4820

European-Finnish (FIN)

AF:

0.102

AC:

1081

AN:

10588

Middle Eastern (MID)

AF:

0.243

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.163

AC:

11085

AN:

68002

Other (OTH)

AF:

0.172

AC:

363

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

950

1900

2849

3799

4749

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.166

Hom.:

4401

Bravo

AF:

0.151

Asia WGS

AF:

0.233

AC:

810

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.022

(source)

DANN

Benign

0.51

PhyloP100

-0.51

Mutation Taster

=100/0

polymorphism (auto)

(source)

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