16-14951787-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_006985.4(NPIPA1):c.815C>A(p.Thr272Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000747 in 132,576 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T272S) has been classified as Likely benign.
Frequency
Consequence
NM_006985.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPIPA1 | NM_006985.4 | c.815C>A | p.Thr272Asn | missense_variant | 8/8 | ENST00000328085.10 | |
PKD1P3-NPIPA1 | NR_146231.1 | n.7092C>A | non_coding_transcript_exon_variant | 39/39 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPIPA1 | ENST00000328085.10 | c.815C>A | p.Thr272Asn | missense_variant | 8/8 | 1 | NM_006985.4 | P1 | |
NPIPA1 | ENST00000472413.5 | n.5072C>A | non_coding_transcript_exon_variant | 28/28 | 2 | ||||
NPIPA1 | ENST00000541836.5 | n.2660C>A | non_coding_transcript_exon_variant | 20/20 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000732 AC: 97AN: 132506Hom.: 3 Cov.: 23
GnomAD3 exomes AF: 0.00114 AC: 235AN: 206122Hom.: 18 AF XY: 0.00108 AC XY: 122AN XY: 112450
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00858 AC: 11362AN: 1323906Hom.: 7 Cov.: 33 AF XY: 0.00862 AC XY: 5675AN XY: 658562
GnomAD4 genome AF: 0.000747 AC: 99AN: 132576Hom.: 3 Cov.: 23 AF XY: 0.000608 AC XY: 39AN XY: 64194
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 28, 2023 | The c.815C>A (p.T272N) alteration is located in exon 8 (coding exon 8) of the NPIPA1 gene. This alteration results from a C to A substitution at nucleotide position 815, causing the threonine (T) at amino acid position 272 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | NPIPA1: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at