rs10806425

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000257749.9(BACH2):​c.-274-10212G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,882 control chromosomes in the GnomAD database, including 8,920 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 ( 8920 hom., cov: 31)

Consequence

BACH2
ENST00000257749.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.815
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BACH2NM_021813.4 linkuse as main transcriptc.-274-10212G>T intron_variant ENST00000257749.9 NP_068585.1
BACH2NM_001170794.2 linkuse as main transcriptc.-274-10212G>T intron_variant NP_001164265.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BACH2ENST00000257749.9 linkuse as main transcriptc.-274-10212G>T intron_variant 1 NM_021813.4 ENSP00000257749 P1

Frequencies

GnomAD3 genomes
AF:
0.328
AC:
49835
AN:
151764
Hom.:
8919
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.224
Gnomad AMI
AF:
0.449
Gnomad AMR
AF:
0.377
Gnomad ASJ
AF:
0.444
Gnomad EAS
AF:
0.0846
Gnomad SAS
AF:
0.357
Gnomad FIN
AF:
0.265
Gnomad MID
AF:
0.358
Gnomad NFE
AF:
0.399
Gnomad OTH
AF:
0.349
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.328
AC:
49848
AN:
151882
Hom.:
8920
Cov.:
31
AF XY:
0.322
AC XY:
23867
AN XY:
74226
show subpopulations
Gnomad4 AFR
AF:
0.224
Gnomad4 AMR
AF:
0.377
Gnomad4 ASJ
AF:
0.444
Gnomad4 EAS
AF:
0.0850
Gnomad4 SAS
AF:
0.360
Gnomad4 FIN
AF:
0.265
Gnomad4 NFE
AF:
0.399
Gnomad4 OTH
AF:
0.345
Alfa
AF:
0.387
Hom.:
25158
Bravo
AF:
0.332
Asia WGS
AF:
0.216
AC:
753
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.79
DANN
Benign
0.72

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10806425; hg19: chr6-90926612; COSMIC: COSV57606519; API