rs10491211
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020772.3(NUFIP2):c.2002+5748T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000578 in 152,230 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00058 ( 0 hom., cov: 32)
Consequence
NUFIP2
NM_020772.3 intron
NM_020772.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.539
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUFIP2 | NM_020772.3 | c.2002+5748T>G | intron_variant | ENST00000225388.9 | |||
NUFIP2 | XM_017024896.3 | c.1525+5748T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUFIP2 | ENST00000225388.9 | c.2002+5748T>G | intron_variant | 1 | NM_020772.3 | P1 | |||
NUFIP2 | ENST00000579665.1 | c.278-12714T>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000578 AC: 88AN: 152230Hom.: 0 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: 0.000578 AC: 88AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000605 AC XY: 45AN XY: 74366
GnomAD4 genome
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88
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32
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45
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74366
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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