chr2-121727863-T-TGA
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_032390.5(NIFK):c.741_742dupTC(p.Gln248fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000844 in 1,606,770 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00081 ( 3 hom. )
Consequence
NIFK
NM_032390.5 frameshift
NM_032390.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.454
Genes affected
NIFK (HGNC:17838): (nucleolar protein interacting with the FHA domain of MKI67) This gene encodes a protein that interacts with the forkhead-associated domain of the Ki-67 antigen. The encoded protein may bind RNA and may play a role in mitosis and cell cycle progression. Multiple pseudogenes exist on chromosomes 5, 10, 12, 15, and 19.[provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 2-121727863-T-TGA is Benign according to our data. Variant chr2-121727863-T-TGA is described in ClinVar as [Likely_benign]. Clinvar id is 719899.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NIFK | NM_032390.5 | c.741_742dupTC | p.Gln248fs | frameshift_variant | 7/7 | ENST00000285814.9 | NP_115766.3 | |
NIFK-AS1 | NR_037857.1 | n.1147_1148dupGA | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NIFK | ENST00000285814.9 | c.741_742dupTC | p.Gln248fs | frameshift_variant | 7/7 | 1 | NM_032390.5 | ENSP00000285814.4 |
Frequencies
GnomAD3 genomes AF: 0.00114 AC: 174AN: 152182Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000800 AC: 198AN: 247540Hom.: 0 AF XY: 0.000777 AC XY: 104AN XY: 133776
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GnomAD4 exome AF: 0.000813 AC: 1182AN: 1454470Hom.: 3 Cov.: 31 AF XY: 0.000836 AC XY: 605AN XY: 723616
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GnomAD4 genome AF: 0.00114 AC: 174AN: 152300Hom.: 2 Cov.: 32 AF XY: 0.00122 AC XY: 91AN XY: 74468
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 03, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at