Variant chr4-101830119-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_017935.5(BANK1):c.382C>T(p.Leu128Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 1,610,998 control chromosomes in the GnomAD database, including 138,341 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 0.49 ( 19556 hom., cov: 32)

Exomes 𝑓: 0.40 ( 118785 hom. )

Consequence

BANK1
NM_017935.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0260

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP7

Synonymous conserved (PhyloP=0.026 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BANK1	NM_017935.5 linkuse as main transcript	c.382C>T	p.Leu128Leu	synonymous_variant	2/17	ENST00000322953.9	NP_060405.5	Q8NDB2-1
BANK1	NM_001083907.3 linkuse as main transcript	c.292C>T	p.Leu98Leu	synonymous_variant	2/17		NP_001077376.3	Q8NDB2-3
BANK1	NM_001127507.3 linkuse as main transcript	c.71-24916C>T		intron_variant			NP_001120979.3	Q8NDB2-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9 linkuse as main transcript	c.382C>T	p.Leu128Leu	synonymous_variant	2/17	1	NM_017935.5	ENSP00000320509.4		Q8NDB2-1

Frequencies

GnomAD3 genomes

AF:

0.486

AC:

73835

AN:

151948

Hom.:

19518

Cov.:

show subpopulations

Gnomad AFR

AF:

0.702

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.477

Gnomad EAS

AF:

0.473

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.377

Gnomad OTH

AF:

0.466

GnomAD3 exomes

AF:

0.428

AC:

106137

AN:

248068

Hom.:

23716

AF XY:

0.420

AC XY:

56406

AN XY:

134270

show subpopulations

Gnomad AFR exome

AF:

0.715

Gnomad AMR exome

AF:

0.448

Gnomad ASJ exome

AF:

0.475

Gnomad EAS exome

AF:

0.475

Gnomad SAS exome

AF:

0.443

Gnomad FIN exome

AF:

0.383

Gnomad NFE exome

AF:

0.375

Gnomad OTH exome

AF:

0.408

GnomAD4 exome

AF:

0.399

AC:

581622

AN:

1458932

Hom.:

118785

Cov.:

AF XY:

0.399

AC XY:

289725

AN XY:

725660

show subpopulations

Gnomad4 AFR exome

AF:

0.711

Gnomad4 AMR exome

AF:

0.455

Gnomad4 ASJ exome

AF:

0.479

Gnomad4 EAS exome

AF:

0.417

Gnomad4 SAS exome

AF:

0.437

Gnomad4 FIN exome

AF:

0.378

Gnomad4 NFE exome

AF:

0.381

Gnomad4 OTH exome

AF:

0.430

GnomAD4 genome

AF:

0.486

AC:

73926

AN:

152066

Hom.:

19556

Cov.:

AF XY:

0.488

AC XY:

36252

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.702

Gnomad4 AMR

AF:

0.484

Gnomad4 ASJ

AF:

0.477

Gnomad4 EAS

AF:

0.473

Gnomad4 SAS

AF:

0.465

Gnomad4 FIN

AF:

0.386

Gnomad4 NFE

AF:

0.377

Gnomad4 OTH

AF:

0.470

Alfa

AF:

0.418

Hom.:

15081

Bravo

AF:

0.498

Asia WGS

AF:

0.525

AC:

1823

AN:

3474

EpiCase

AF:

0.386

EpiControl

AF:

0.387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.6

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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