rs1055403

Variant names:

• chr6-89929244-G-A
• rs1055403
• NM_021813.4:c.*3164C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-89929244-G-A
• chr6-89929244-G-C
• chr6-89929244-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 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=-0.85).
• 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 rank	MANE	Protein	UniProt
BACH2	NM_021813.4	c.*3164C>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000257749.9	NP_068585.1
BACH2	NM_001170794.2	c.*3164C>T		3_prime_UTR_variant	Exon 7 of 7		NP_001164265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BACH2	ENST00000257749.9	c.*3164C>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_021813.4	ENSP00000257749.4

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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.174 AC: 24 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0895 AC: 3716 AN: 41502

American (AMR) AF: 0.178 AC: 2718 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1065 AN: 5164

South Asian (SAS) AF: 0.255 AC: 1230 AN: 4820

European-Finnish (FIN) AF: 0.102 AC: 1081 AN: 10588

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11085 AN: 68002

Other (OTH) AF: 0.172 AC: 363 AN: 2110

Alfa AF: 0.166 Hom.: 4401

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
PhyloP100		-0.51
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: rs1055403; hg19: chr6-90638963;