Genetic Variant BANK1:c.1900+2259T>G (chr4-102032524-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017935.5(BANK1):c.1900+2259T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,908 control chromosomes in the GnomAD database, including 33,520 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 0.66 ( 33517 hom., cov: 31)

Exomes 𝑓: 1.0 ( 3 hom. )

Consequence

BANK1
NM_017935.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.217

Publications

5 publications found

Variant links:

Genes affected

BANK1 (HGNC:18233): (B cell scaffold protein with ankyrin repeats 1) The protein encoded by this gene is a B-cell-specific scaffold protein that functions in B-cell receptor-induced calcium mobilization from intracellular stores. This protein can also promote Lyn-mediated tyrosine phosphorylation of inositol 1,4,5-trisphosphate receptors. Polymorphisms in this gene are associated with susceptibility to systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

BANK1 Gene-Disease associations (from GenCC):

systemic lupus erythematosus
Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

BANK1 links:

ENSG00000251309 (HGNC:):

ENSG00000251309 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
BANK1	NM_017935.5 link	c.1900+2259T>G	intron_variant	Intron 10 of 16	ENST00000322953.9	NP_060405.5
BANK1	NM_001083907.3 link	c.1810+2259T>G	intron_variant	Intron 10 of 16		NP_001077376.3
BANK1	NM_001127507.3 link	c.1501+2259T>G	intron_variant	Intron 9 of 15		NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9 link	c.1900+2259T>G		intron_variant	Intron 10 of 16	1	NM_017935.5	ENSP00000320509.4

Frequencies

GnomAD3 genomes

AF:

0.659

AC:

100004

AN:

151784

Hom.:

33487

Cov.:

show subpopulations

Gnomad AFR

AF:

0.780

Gnomad AMI

AF:

0.684

Gnomad AMR

AF:

0.680

Gnomad ASJ

AF:

0.665

Gnomad EAS

AF:

0.636

Gnomad SAS

AF:

0.636

Gnomad FIN

AF:

0.533

Gnomad MID

AF:

0.618

Gnomad NFE

AF:

0.602

Gnomad OTH

AF:

0.683

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.659

AC:

100081

AN:

151902

Hom.:

33517

Cov.:

AF XY:

0.654

AC XY:

48549

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.780

AC:

32302

AN:

41410

American (AMR)

AF:

0.679

AC:

10365

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.665

AC:

2308

AN:

3470

East Asian (EAS)

AF:

0.637

AC:

3291

AN:

5164

South Asian (SAS)

AF:

0.636

AC:

3059

AN:

4810

European-Finnish (FIN)

AF:

0.533

AC:

5626

AN:

10550

Middle Eastern (MID)

AF:

0.623

AC:

182

AN:

292

European-Non Finnish (NFE)

AF:

0.602

AC:

40884

AN:

67928

Other (OTH)

AF:

0.683

AC:

1443

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1695

3391

5086

6782

8477

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.625

Hom.:

27475

Bravo

AF:

0.675

Asia WGS

AF:

0.667

AC:

2325

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

8.9

(source)

DANN

Benign

0.78

PhyloP100

-0.22

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over