chr6-90119163-T-C

Position:

• chr6-90119163-T-C

Variant summary

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

The ENST00000257749.9(BACH2):​c.-161-30054A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,086 control chromosomes in the GnomAD database, including 18,197 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 0.48 (18197 hom., cov: 32)
• Consequence: BACH2 ENST00000257749.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BACH2	NM_021813.4	c.-161-30054A>G		intron_variant		ENST00000257749.9	NP_068585.1
BACH2	NM_001170794.2	c.-161-30054A>G		intron_variant			NP_001164265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BACH2	ENST00000257749.9	c.-161-30054A>G		intron_variant		1	NM_021813.4	ENSP00000257749	P1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73050 AN: 151968 Hom.: 18168 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.481 AC: 73133 AN: 152086 Hom.: 18197 Cov.: 32 AF XY: 0.478 AC XY: 35568 AN XY: 74362

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.477

Alfa AF: 0.445 Hom.: 14674

Bravo AF: 0.494

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.82

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: rs207270; hg19: chr6-90828882;