rs10806416

Variant names:

• chr6-89989101-T-C
• rs10806416
• NM_021813.4:c.243+19501A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021813.4(BACH2):​c.243+19501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,082 control chromosomes in the GnomAD database, including 8,617 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 0.33 (8617 hom., cov: 32)
• Consequence: BACH2 NM_021813.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 4 publications found

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 Gene-Disease associations (from GenCC):

• immunodeficiency 60

  Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Illumina, ClinGen, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021813.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BACH2	NM_021813.4	MANE Select	c.243+19501A>G		intron	N/A	NP_068585.1
	BACH2	NM_001170794.2		c.243+19501A>G		intron	N/A	NP_001164265.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BACH2	ENST00000257749.9	TSL:1 MANE Select	c.243+19501A>G		intron	N/A	ENSP00000257749.4
	BACH2	ENST00000343122.7	TSL:5	c.243+19501A>G		intron	N/A	ENSP00000345642.3
	BACH2	ENST00000406998.7	TSL:2	c.243+19501A>G		intron	N/A	ENSP00000384145.3

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49595 AN: 151964 Hom.: 8612 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0608

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.326 AC: 49615 AN: 152082 Hom.: 8617 Cov.: 32 AF XY: 0.322 AC XY: 23927 AN XY: 74348

African (AFR) AF: 0.309 AC: 12831 AN: 41458

American (AMR) AF: 0.260 AC: 3971 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3472

East Asian (EAS) AF: 0.0605 AC: 313 AN: 5172

South Asian (SAS) AF: 0.298 AC: 1434 AN: 4820

European-Finnish (FIN) AF: 0.343 AC: 3624 AN: 10580

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25090 AN: 67970

Other (OTH) AF: 0.347 AC: 733 AN: 2114

Alfa AF: 0.354 Hom.: 16242

Bravo AF: 0.318

Asia WGS AF: 0.200 AC: 694 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.80
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10806416; hg19: chr6-90698820; COSMIC: COSV57605657;