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rs10516487

Variant summary

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

The NM_017935.5(BANK1):c.182G>A(p.Arg61His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,612,802 control chromosomes in the GnomAD database, including 69,684 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R61C) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.27 ( 5617 hom., cov: 32)
Exomes 𝑓: 0.29 ( 64067 hom. )

Consequence

BANK1
NM_017935.5 missense

Scores

1
15

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.566
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]

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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 (MetaRNN=0.0013894141).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BANK1NM_017935.5 linkuse as main transcriptc.182G>A p.Arg61His missense_variant 2/17 ENST00000322953.9
BANK1NM_001083907.3 linkuse as main transcriptc.92G>A p.Arg31His missense_variant 2/17
BANK1NM_001127507.3 linkuse as main transcriptc.71-25116G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BANK1ENST00000322953.9 linkuse as main transcriptc.182G>A p.Arg61His missense_variant 2/171 NM_017935.5 P1Q8NDB2-1

Frequencies

GnomAD3 genomes
AF:
0.268
AC:
40693
AN:
151914
Hom.:
5621
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.238
Gnomad AMI
AF:
0.171
Gnomad AMR
AF:
0.223
Gnomad ASJ
AF:
0.351
Gnomad EAS
AF:
0.163
Gnomad SAS
AF:
0.188
Gnomad FIN
AF:
0.323
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.298
Gnomad OTH
AF:
0.267
GnomAD3 exomes
AF:
0.257
AC:
64596
AN:
251048
Hom.:
8904
AF XY:
0.258
AC XY:
34963
AN XY:
135690
show subpopulations
Gnomad AFR exome
AF:
0.238
Gnomad AMR exome
AF:
0.175
Gnomad ASJ exome
AF:
0.350
Gnomad EAS exome
AF:
0.167
Gnomad SAS exome
AF:
0.188
Gnomad FIN exome
AF:
0.321
Gnomad NFE exome
AF:
0.297
Gnomad OTH exome
AF:
0.273
GnomAD4 exome
AF:
0.291
AC:
424976
AN:
1460770
Hom.:
64067
Cov.:
35
AF XY:
0.289
AC XY:
209939
AN XY:
726706
show subpopulations
Gnomad4 AFR exome
AF:
0.232
Gnomad4 AMR exome
AF:
0.177
Gnomad4 ASJ exome
AF:
0.347
Gnomad4 EAS exome
AF:
0.129
Gnomad4 SAS exome
AF:
0.189
Gnomad4 FIN exome
AF:
0.315
Gnomad4 NFE exome
AF:
0.309
Gnomad4 OTH exome
AF:
0.290
GnomAD4 genome
AF:
0.268
AC:
40711
AN:
152032
Hom.:
5617
Cov.:
32
AF XY:
0.266
AC XY:
19730
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.238
Gnomad4 AMR
AF:
0.223
Gnomad4 ASJ
AF:
0.351
Gnomad4 EAS
AF:
0.162
Gnomad4 SAS
AF:
0.189
Gnomad4 FIN
AF:
0.323
Gnomad4 NFE
AF:
0.298
Gnomad4 OTH
AF:
0.268
Alfa
AF:
0.290
Hom.:
12204
Bravo
AF:
0.257
TwinsUK
AF:
0.317
AC:
1177
ALSPAC
AF:
0.312
AC:
1204
ESP6500AA
AF:
0.244
AC:
1075
ESP6500EA
AF:
0.303
AC:
2610
ExAC
AF:
0.255
AC:
30903
Asia WGS
AF:
0.205
AC:
715
AN:
3478
EpiCase
AF:
0.307
EpiControl
AF:
0.303

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Variant of unknown significance Uncertain:1
Uncertain significance, no assertion criteria providedliterature onlyOMIMSep 15, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.071
BayesDel_addAF
Benign
-0.78
T
BayesDel_noAF
Benign
-0.75
Cadd
Benign
10
Dann
Uncertain
0.98
Eigen
Benign
-0.94
Eigen_PC
Benign
-0.93
FATHMM_MKL
Benign
0.022
N
LIST_S2
Benign
0.54
T;T;T
MetaRNN
Benign
0.0014
T;T;T
MetaSVM
Benign
-0.91
T
MutationTaster
Benign
1.0
P;P;P;P;P
PrimateAI
Benign
0.17
T
PROVEAN
Benign
-1.4
N;N;N
REVEL
Benign
0.077
Sift
Benign
0.11
T;T;T
Sift4G
Benign
0.62
T;T;T
Polyphen
0.060
B;B;.
Vest4
0.013
MPC
0.023
ClinPred
0.0074
T
GERP RS
-1.2
Varity_R
0.042
gMVP
0.15

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: rs10516487; hg19: chr4-102751076; COSMIC: COSV59840716; API