rs1059177
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_001395485.2(NPIPA2):āc.933T>Cā(p.Cys311=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.0020 ( 0 hom., cov: 18)
Exomes š: 0.00029 ( 8 hom. )
Failed GnomAD Quality Control
Consequence
NPIPA2
NM_001395485.2 synonymous
NM_001395485.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.22
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BP7
?
Synonymous conserved (PhyloP=-2.22 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPIPA2 | NM_001395485.2 | c.933T>C | p.Cys311= | synonymous_variant | 10/10 | ENST00000529166.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPIPA2 | ENST00000529166.6 | c.933T>C | p.Cys311= | synonymous_variant | 10/10 | 5 | NM_001395485.2 | P1 | |
NPIPA2 | ENST00000553201.1 | c.876T>C | p.Cys292= | synonymous_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 249AN: 123100Hom.: 0 Cov.: 18 FAILED QC
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GnomAD3 exomes AF: 0.000827 AC: 50AN: 60458Hom.: 1 AF XY: 0.000609 AC XY: 18AN XY: 29578
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000288 AC: 398AN: 1381774Hom.: 8 Cov.: 28 AF XY: 0.000243 AC XY: 168AN XY: 690808
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00204 AC: 251AN: 123188Hom.: 0 Cov.: 18 AF XY: 0.00202 AC XY: 120AN XY: 59394
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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