11-66002942-G-A

Position:

• chr11-66002942-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003860.4(BANF1):​c.-16-293G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 407,568 control chromosomes in the GnomAD database, including 41,236 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.42 (13973 hom., cov: 31)
  • Exomes 𝑓: 0.46 (27263 hom.)
• Consequence: BANF1 NM_003860.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.31

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 11-66002942-G-A is Benign according to our data. Variant chr11-66002942-G-A is described in ClinVar as [Benign]. Clinvar id is 1272135.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BANF1	NM_003860.4	c.-16-293G>A		intron_variant		ENST00000312175.7	NP_003851.1
BANF1	NM_001143985.1	c.-16-293G>A		intron_variant			NP_001137457.1
BANF1	XM_017018515.3	c.-17+107G>A		intron_variant			XP_016874004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BANF1	ENST00000312175.7	c.-16-293G>A		intron_variant		1	NM_003860.4	ENSP00000310275	P1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63908 AN: 151902 Hom.: 13968 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.430

GnomAD4 exome AF: 0.456 AC: 116475 AN: 255548 Hom.: 27263 Cov.: 2 AF XY: 0.452 AC XY: 62242 AN XY: 137676

Gnomad4 AFR exome AF: 0.314

Gnomad4 AMR exome AF: 0.618

Gnomad4 ASJ exome AF: 0.474

Gnomad4 EAS exome AF: 0.541

Gnomad4 SAS exome AF: 0.439

Gnomad4 FIN exome AF: 0.401

Gnomad4 NFE exome AF: 0.449

Gnomad4 OTH exome AF: 0.464

GnomAD4 genome AF: 0.421 AC: 63945 AN: 152020 Hom.: 13973 Cov.: 31 AF XY: 0.421 AC XY: 31304 AN XY: 74294

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.432

Alfa AF: 0.434 Hom.: 2969

Bravo AF: 0.433

Asia WGS AF: 0.505 AC: 1755 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.1
DANN	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs12794370; hg19: chr11-65770413;