rs2967682
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001378600.1(NFILZ):c.-163-854A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,820 control chromosomes in the GnomAD database, including 38,368 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.70 ( 38368 hom., cov: 31)
Consequence
NFILZ
NM_001378600.1 intron
NM_001378600.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.48
Genes affected
NFILZ (HGNC:52681): (NFIL3 like basic leucine zipper) Predicted to enable DNA binding activity and DNA-binding transcription factor activity. Predicted to be involved in immune response; regulation of transcription, DNA-templated; and transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFILZ | NM_001378600.1 | c.-163-854A>C | intron_variant | ENST00000691075.1 | |||
NFILZ | NM_001378599.1 | c.-163-854A>C | intron_variant | ||||
NFILZ | NM_001378601.1 | c.-65-854A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFILZ | ENST00000691075.1 | c.-163-854A>C | intron_variant | NM_001378600.1 | P1 | ||||
NFILZ | ENST00000570582.4 | c.-157-854A>C | intron_variant | P1 | |||||
NFILZ | ENST00000671902.2 | c.-161-854A>C | intron_variant | P1 | |||||
NFILZ | ENST00000673603.2 | c.-163-854A>C | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.700 AC: 106139AN: 151702Hom.: 38317 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.700 AC: 106246AN: 151820Hom.: 38368 Cov.: 31 AF XY: 0.704 AC XY: 52235AN XY: 74180
GnomAD4 genome
?
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106246
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74180
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at