rs56984820

Variant names:

• chr11-66003579-TCACTGAG-T
• rs56984820
• NM_003860.4:c.124-37_124-31delCTGAGCA

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003860.4(BANF1):​c.124-37_124-31delCTGAGCA 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
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• Nestor-Guillermo progeria syndrome

  Inheritance: AR, Unknown Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.
• 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 rank	MANE	Protein	UniProt
BANF1	NM_003860.4	c.124-37_124-31delCTGAGCA		intron_variant	Intron 2 of 2	ENST00000312175.7	NP_003851.1
BANF1	NM_001143985.2	c.124-37_124-31delCTGAGCA		intron_variant	Intron 2 of 2		NP_001137457.1
BANF1	NM_001440618.1	c.124-37_124-31delCTGAGCA		intron_variant	Intron 2 of 2		NP_001427547.1
BANF1	NM_001440619.1	c.124-37_124-31delCTGAGCA		intron_variant	Intron 2 of 2		NP_001427548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANF1	ENST00000312175.7	c.124-46_124-40delCACTGAG		intron_variant	Intron 2 of 2	1	NM_003860.4	ENSP00000310275.2

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

GnomAD2 exomes AF: 0.463 AC: 114912 AN: 247934 AF XY: 0.456

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 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

African (AFR) AF: 0.305 AC: 10205 AN: 33472

American (AMR) AF: 0.660 AC: 29469 AN: 44674

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 12302 AN: 26132

East Asian (EAS) AF: 0.562 AC: 22291 AN: 39686

South Asian (SAS) AF: 0.442 AC: 38062 AN: 86132

European-Finnish (FIN) AF: 0.390 AC: 20786 AN: 53298

Middle Eastern (MID) AF: 0.374 AC: 2130 AN: 5702

European-Non Finnish (NFE) AF: 0.461 AC: 512151 AN: 1111608

Other (OTH) AF: 0.461 AC: 27844 AN: 60378

GnomAD4 genome AF: 0.419 AC: 63341 AN: 151298 Hom.: 13701 Cov.: 0 AF XY: 0.419 AC XY: 30994 AN XY: 73928

African (AFR) AF: 0.309 AC: 12740 AN: 41288

American (AMR) AF: 0.562 AC: 8526 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1637 AN: 3446

East Asian (EAS) AF: 0.518 AC: 2629 AN: 5080

South Asian (SAS) AF: 0.450 AC: 2162 AN: 4806

European-Finnish (FIN) AF: 0.375 AC: 3943 AN: 10508

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30229 AN: 67706

Other (OTH) AF: 0.429 AC: 898 AN: 2094

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

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.76
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs56984820; hg19: chr11-65771050; COSMIC: COSV56463283; COSMIC: COSV56463283;