rs7168431
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_016359.5(NUSAP1):āc.1326A>Gā(p.Ter442=) variant causes a stop retained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 1,554,700 control chromosomes in the GnomAD database, including 46,136 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: š 0.18 ( 3372 hom., cov: 31)
Exomes š: 0.24 ( 42764 hom. )
Consequence
NUSAP1
NM_016359.5 stop_retained
NM_016359.5 stop_retained
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.02
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP7
?
Synonymous conserved (PhyloP=1.02 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUSAP1 | NM_016359.5 | c.1326A>G | p.Ter442= | stop_retained_variant | 11/11 | ENST00000559596.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUSAP1 | ENST00000559596.6 | c.1326A>G | p.Ter442= | stop_retained_variant | 11/11 | 1 | NM_016359.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.185 AC: 28058AN: 151770Hom.: 3374 Cov.: 31
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GnomAD3 exomes AF: 0.209 AC: 35540AN: 170256Hom.: 4365 AF XY: 0.212 AC XY: 19110AN XY: 90184
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GnomAD4 exome AF: 0.239 AC: 335027AN: 1402812Hom.: 42764 Cov.: 28 AF XY: 0.238 AC XY: 165178AN XY: 693224
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GnomAD4 genome ? AF: 0.185 AC: 28049AN: 151888Hom.: 3372 Cov.: 31 AF XY: 0.186 AC XY: 13797AN XY: 74170
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at