Variant rs56984820 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003860.4(BANF1):c.124-37_124-31del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 1,612,380 control chromosomes in the GnomAD database, including 172,060 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.42 ( 13701 hom., cov: 0)

Exomes 𝑓: 0.46 ( 158359 hom. )

Consequence

BANF1
NM_003860.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.759

Variant links:

Genes affected

BANF1 (HGNC:17397): (BAF nuclear assembly factor 1) The protein encoded by this gene was first identified by its ability to protect retroviruses from intramolecular integration and therefore promote intermolecular integration into the host cell genome. The protein forms a homodimer which localizes to both the nucleus and cytoplasm and is specifically associated with chromosomes during mitosis. This protein binds to double stranded DNA in a non-specific manner and also binds to LEM-domain containing proteins of the nuclear envelope. This protein is thought to facilitate nuclear reassembly by binding with both DNA and inner nuclear membrane proteins and thereby recruit chromatin to the nuclear periphery. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Jan 2009]

BANF1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-66003579-TCACTGAG-T is Benign according to our data. Variant chr11-66003579-TCACTGAG-T is described in ClinVar as [Benign]. Clinvar id is 1266005.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-66003579-TCACTGAG-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
BANF1	NM_003860.4 linkuse as main transcript	c.124-37_124-31del	intron_variant	ENST00000312175.7	NP_003851.1
BANF1	NM_001143985.1 linkuse as main transcript	c.124-37_124-31del	intron_variant		NP_001137457.1
BANF1	XM_017018515.3 linkuse as main transcript	c.124-37_124-31del	intron_variant		XP_016874004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BANF1	ENST00000312175.7 linkuse as main transcript	c.124-37_124-31del		intron_variant		1	NM_003860.4	ENSP00000310275	P1

Frequencies

GnomAD3 genomes

AF:

0.419

AC:

63302

AN:

151178

Hom.:

13694

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.562

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.516

Gnomad SAS

AF:

0.450

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.366

Gnomad NFE

AF:

0.446

Gnomad OTH

AF:

0.427

GnomAD3 exomes

AF:

0.463

AC:

114912

AN:

247934

Hom.:

27439

AF XY:

0.456

AC XY:

61156

AN XY:

134236

show subpopulations

Gnomad AFR exome

AF:

0.311

Gnomad AMR exome

AF:

0.667

Gnomad ASJ exome

AF:

0.475

Gnomad EAS exome

AF:

0.500

Gnomad SAS exome

AF:

0.442

Gnomad FIN exome

AF:

0.379

Gnomad NFE exome

AF:

0.438

Gnomad OTH exome

AF:

0.456

GnomAD4 exome

AF:

0.462

AC:

675240

AN:

1461082

Hom.:

158359

AF XY:

0.460

AC XY:

334143

AN XY:

726860

show subpopulations

Gnomad4 AFR exome

AF:

0.305

Gnomad4 AMR exome

AF:

0.660

Gnomad4 ASJ exome

AF:

0.471

Gnomad4 EAS exome

AF:

0.562

Gnomad4 SAS exome

AF:

0.442

Gnomad4 FIN exome

AF:

0.390

Gnomad4 NFE exome

AF:

0.461

Gnomad4 OTH exome

AF:

0.461

GnomAD4 genome

AF:

0.419

AC:

63341

AN:

151298

Hom.:

13701

Cov.:

AF XY:

0.419

AC XY:

30994

AN XY:

73928

show subpopulations

Gnomad4 AFR

AF:

0.309

Gnomad4 AMR

AF:

0.562

Gnomad4 ASJ

AF:

0.475

Gnomad4 EAS

AF:

0.518

Gnomad4 SAS

AF:

0.450

Gnomad4 FIN

AF:

0.375

Gnomad4 NFE

AF:

0.446

Gnomad4 OTH

AF:

0.429

Alfa

AF:

0.361

Hom.:

1607

Bravo

AF:

0.434

Asia WGS

AF:

0.506

AC:

1757

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over