rs56984820
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
NM_003860.4 intron
Scores
Not classified
Clinical Significance
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]
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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 | 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: 63302AN: 151178Hom.: 13694 Cov.: 0
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GnomAD3 exomes AF: 0.463 AC: 114912AN: 247934Hom.: 27439 AF XY: 0.456 AC XY: 61156AN XY: 134236
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GnomAD4 exome AF: 0.462 AC: 675240AN: 1461082Hom.: 158359 AF XY: 0.460 AC XY: 334143AN XY: 726860
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GnomAD4 genome ? AF: 0.419 AC: 63341AN: 151298Hom.: 13701 Cov.: 0 AF XY: 0.419 AC XY: 30994AN XY: 73928
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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
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at