rs56984820

Positions:

• chr11-66003579-TCACTGAG-T
• chr11-66003579-TCACTGAG-TCACTGAGCACTGAG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.759

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]

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	UniProt
BANF1	NM_003860.4	c.124-37_124-31del		intron_variant		ENST00000312175.7
BANF1	NM_001143985.1	c.124-37_124-31del		intron_variant
BANF1	XM_017018515.3	c.124-37_124-31del		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63302 AN: 151178 Hom.: 13694 Cov.: 0

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

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

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.: 0 AF XY: 0.419 AC XY: 30994 AN XY: 73928

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs56984820; hg19: chr11-65771050;