rs1055403

Positions:

• chr6-89929244-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BACH2	NM_021813.4	c.*3164C>T		3_prime_UTR_variant	9/9	ENST00000257749.9	NP_068585.1
BACH2	NM_001170794.2	c.*3164C>T		3_prime_UTR_variant	7/7		NP_001164265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BACH2	ENST00000257749.9	c.*3164C>T		3_prime_UTR_variant	9/9	1	NM_021813.4	ENSP00000257749	P1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22207 AN: 152018 Hom.: 1844 Cov.: 32

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: 27 AN: 158 Hom.: 2 Cov.: 0 AF XY: 0.178 AC XY: 16 AN XY: 90

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.174

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.146 AC: 22220 AN: 152136 Hom.: 1846 Cov.: 32 AF XY: 0.146 AC XY: 10887 AN XY: 74350

Gnomad4 AFR AF: 0.0895

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.172

Alfa AF: 0.170 Hom.: 3090

Bravo AF: 0.151

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.022
DANN	Benign	0.51

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

LitVar

Other links and lift over

dbSNP: rs1055403; hg19: chr6-90638963;