rs7695738

Variant summary

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

The ENST00000504592.5(BANK1):​c.26-49733G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,258 control chromosomes in the GnomAD database, including 1,428 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 0.13 ( 1428 hom., cov: 32)

Consequence

BANK1
ENST00000504592.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.335
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 (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BANK1ENST00000504592.5 linkc.26-49733G>A intron_variant Intron 5 of 20 2 ENSP00000421443.1 Q8NDB2-2

Frequencies

GnomAD3 genomes
AF:
0.131
AC:
20000
AN:
152140
Hom.:
1420
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.156
Gnomad AMI
AF:
0.0396
Gnomad AMR
AF:
0.140
Gnomad ASJ
AF:
0.0896
Gnomad EAS
AF:
0.175
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.0739
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.125
Gnomad OTH
AF:
0.132
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.132
AC:
20037
AN:
152258
Hom.:
1428
Cov.:
32
AF XY:
0.128
AC XY:
9567
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.156
Gnomad4 AMR
AF:
0.142
Gnomad4 ASJ
AF:
0.0896
Gnomad4 EAS
AF:
0.176
Gnomad4 SAS
AF:
0.109
Gnomad4 FIN
AF:
0.0739
Gnomad4 NFE
AF:
0.125
Gnomad4 OTH
AF:
0.131
Alfa
AF:
0.127
Hom.:
1794
Bravo
AF:
0.138
Asia WGS
AF:
0.139
AC:
483
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.6
DANN
Benign
0.67

Splicing

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: rs7695738; hg19: chr4-102701232; API