Variant rs9344996 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021813.4(BACH2):c.-274-12901A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,264 control chromosomes in the GnomAD database, including 1,088 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 0.099 ( 1088 hom., cov: 32)

Consequence

BACH2
NM_021813.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.507

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]

BACH2 links:

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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=-0.5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BACH2	NM_021813.4 linkuse as main transcript	c.-274-12901A>G		intron_variant		ENST00000257749.9	NP_068585.1
BACH2	NM_001170794.2 linkuse as main transcript	c.-274-12901A>G		intron_variant			NP_001164265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BACH2	ENST00000257749.9 linkuse as main transcript	c.-274-12901A>G		intron_variant		1	NM_021813.4	ENSP00000257749	P1

Frequencies

GnomAD3 genomes

AF:

0.0990

AC:

15064

AN:

152146

Hom.:

1086

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0326

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.0879

Gnomad EAS

AF:

0.357

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0971

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.123

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

GnomAD4 genome

AF:

0.0989

AC:

15059

AN:

152264

Hom.:

1088

Cov.:

AF XY:

0.102

AC XY:

7594

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0325

Gnomad4 AMR

AF:

0.119

Gnomad4 ASJ

AF:

0.0879

Gnomad4 EAS

AF:

0.357

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.0971

Gnomad4 NFE

AF:

0.111

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.111

Hom.:

1082

Bravo

AF:

0.0991

Asia WGS

AF:

0.214

AC:

748

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over