Variant 21-29342954-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001186.4(BACH1):c.*121T>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 0.439 in 966,464 control chromosomes in the GnomAD database, including 96,339 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 0.49 ( 18803 hom., cov: 32)

Exomes 𝑓: 0.43 ( 77536 hom. )

Consequence

BACH1
NM_001186.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.605

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
BACH1	NM_001186.4 linkuse as main transcript	c.*121T>C	3_prime_UTR_variant	5/5	ENST00000286800.8	NP_001177.1
BACH1	NM_206866.3 linkuse as main transcript	c.*121T>C	3_prime_UTR_variant	5/5		NP_996749.1
BACH1	NR_027655.3 linkuse as main transcript	n.1956-8680T>C	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
BACH1	ENST00000286800.8 linkuse as main transcript	c.*121T>C	3_prime_UTR_variant	5/5	1	NM_001186.4	ENSP00000286800	P1
BACH1	ENST00000399921.5 linkuse as main transcript	c.*121T>C	3_prime_UTR_variant	5/5	1		ENSP00000382805	P1
BACH1	ENST00000422809.5 linkuse as main transcript	c.472+13261T>C	intron_variant		5		ENSP00000416569
BACH1	ENST00000468059.1 linkuse as main transcript	c.325+13261T>C	intron_variant		3		ENSP00000470673

Frequencies

GnomAD3 genomes

AF:

0.486

AC:

73922

AN:

151964

Hom.:

18779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.621

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.461

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.484

GnomAD4 exome

AF:

0.430

AC:

350029

AN:

814380

Hom.:

77536

Cov.:

AF XY:

0.433

AC XY:

174167

AN XY:

402252

show subpopulations

Gnomad4 AFR exome

AF:

0.622

Gnomad4 AMR exome

AF:

0.501

Gnomad4 ASJ exome

AF:

0.464

Gnomad4 EAS exome

AF:

0.451

Gnomad4 SAS exome

AF:

0.569

Gnomad4 FIN exome

AF:

0.367

Gnomad4 NFE exome

AF:

0.413

Gnomad4 OTH exome

AF:

0.453

GnomAD4 genome

AF:

0.487

AC:

73990

AN:

152084

Hom.:

18803

Cov.:

AF XY:

0.485

AC XY:

36036

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.621

Gnomad4 AMR

AF:

0.488

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.461

Gnomad4 SAS

AF:

0.596

Gnomad4 FIN

AF:

0.370

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.485

Alfa

AF:

0.441

Hom.:

19258

Bravo

AF:

0.498

Asia WGS

AF:

0.554

AC:

1927

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.1

DANN

Benign

0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over