rs2257055
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022833.4(NIBAN2):c.56-17347T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,066 control chromosomes in the GnomAD database, including 13,930 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 0.41 ( 13930 hom., cov: 32)
Consequence
NIBAN2
NM_022833.4 intron
NM_022833.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.386
Genes affected
NIBAN2 (HGNC:25282): (niban apoptosis regulator 2) Enables transcription coactivator activity. Involved in several processes, including gonadotropin secretion; positive regulation of transcription regulatory region DNA binding activity; and regulation of cellular macromolecule biosynthetic process. Located in several cellular components, including adherens junction; cytosol; and nucleoplasm. [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=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIBAN2 | NM_022833.4 | c.56-17347T>G | intron_variant | ENST00000373312.4 | |||
NIBAN2 | NM_001035534.3 | c.17-17347T>G | intron_variant | ||||
NIBAN2 | XM_005252135.3 | c.274+12023T>G | intron_variant | ||||
NIBAN2 | XM_011518925.2 | c.145+12023T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIBAN2 | ENST00000373312.4 | c.56-17347T>G | intron_variant | 1 | NM_022833.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.408 AC: 61949AN: 151948Hom.: 13933 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.407 AC: 61963AN: 152066Hom.: 13930 Cov.: 32 AF XY: 0.401 AC XY: 29856AN XY: 74366
GnomAD4 genome
?
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32
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29856
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74366
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1334
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at