6-89973325-C-T

Position:

• chr6-89973325-C-T

Variant summary

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

The NM_021813.4(BACH2):​c.244-21463G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,102 control chromosomes in the GnomAD database, including 20,876 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 0.52 (20876 hom., cov: 32)
• Consequence: BACH2 NM_021813.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BACH2	NM_021813.4	c.244-21463G>A		intron_variant		ENST00000257749.9	NP_068585.1
BACH2	NM_001170794.2	c.244-21463G>A		intron_variant			NP_001164265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BACH2	ENST00000257749.9	c.244-21463G>A		intron_variant		1	NM_021813.4	ENSP00000257749.4

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79394 AN: 151984 Hom.: 20850 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.532

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.522 AC: 79452 AN: 152102 Hom.: 20876 Cov.: 32 AF XY: 0.522 AC XY: 38827 AN XY: 74366

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.532

Alfa AF: 0.521 Hom.: 27713

Bravo AF: 0.515

Asia WGS AF: 0.448 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0020
DANN	Benign	0.46

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: rs11969265; hg19: chr6-90683044;