rs886037884
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001277325.2(NPIPA5):c.962C>T(p.Pro321Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000515 in 1,416,716 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001277325.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPIPA5 | NM_001277325.2 | c.962C>T | p.Pro321Leu | missense_variant | 8/8 | ENST00000360151.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPIPA5 | ENST00000360151.9 | c.962C>T | p.Pro321Leu | missense_variant | 8/8 | 1 | NM_001277325.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000953 AC: 12AN: 125868Hom.: 0 Cov.: 24
GnomAD3 exomes AF: 0.0000481 AC: 10AN: 207992Hom.: 1 AF XY: 0.0000611 AC XY: 7AN XY: 114592
GnomAD4 exome AF: 0.0000473 AC: 61AN: 1290758Hom.: 3 Cov.: 37 AF XY: 0.0000515 AC XY: 33AN XY: 641274
GnomAD4 genome ? AF: 0.0000953 AC: 12AN: 125958Hom.: 0 Cov.: 24 AF XY: 0.0000990 AC XY: 6AN XY: 60608
ClinVar
Submissions by phenotype
Oromandibular-limb hypogenesis spectrum Uncertain:1
Uncertain significance, no assertion criteria provided | research | CHU Sainte-Justine Research Center, University of Montreal | Aug 12, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at