rs10944479

chr6-90170674-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.-162+35895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,174 control chromosomes in the GnomAD database, including 1,548 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 0.12 (1548 hom., cov: 32)
• Consequence: BACH2 NM_021813.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BACH2	NM_021813.4	c.-162+35895C>T		intron_variant		ENST00000257749.9
BACH2	NM_001170794.2	c.-162+35895C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BACH2	ENST00000257749.9	c.-162+35895C>T		intron_variant		1	NM_021813.4	P1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18674 AN: 152056 Hom.: 1546 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0797

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.123 AC: 18675 AN: 152174 Hom.: 1548 Cov.: 32 AF XY: 0.117 AC XY: 8724 AN XY: 74390

Gnomad4 AFR AF: 0.0320

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.122

Alfa AF: 0.160 Hom.: 989

Bravo AF: 0.123

Asia WGS AF: 0.0490 AC: 171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	4.1
Dann	Benign	0.78

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: rs10944479; hg19: chr6-90880393;