chr16-14951768-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006985.4(NPIPA1):c.796C>A(p.Pro266Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000432 in 1,503,290 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006985.4 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 |
---|---|---|---|---|---|---|---|
NPIPA1 | NM_006985.4 | c.796C>A | p.Pro266Thr | missense_variant | 8/8 | ENST00000328085.10 | |
PKD1P3-NPIPA1 | NR_146231.1 | n.7073C>A | non_coding_transcript_exon_variant | 39/39 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPIPA1 | ENST00000328085.10 | c.796C>A | p.Pro266Thr | missense_variant | 8/8 | 1 | NM_006985.4 | P1 | |
NPIPA1 | ENST00000472413.5 | n.5053C>A | non_coding_transcript_exon_variant | 28/28 | 2 | ||||
NPIPA1 | ENST00000541836.5 | n.2641C>A | non_coding_transcript_exon_variant | 20/20 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000744 AC: 10AN: 134430Hom.: 0 Cov.: 21
GnomAD3 exomes AF: 0.000110 AC: 23AN: 208834Hom.: 9 AF XY: 0.000114 AC XY: 13AN XY: 113836
GnomAD4 exome AF: 0.0000402 AC: 55AN: 1368860Hom.: 2 Cov.: 32 AF XY: 0.0000440 AC XY: 30AN XY: 681892
GnomAD4 genome AF: 0.0000744 AC: 10AN: 134430Hom.: 0 Cov.: 21 AF XY: 0.0000770 AC XY: 5AN XY: 64970
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 01, 2022 | The c.796C>A (p.P266T) 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 796, causing the proline (P) at amino acid position 266 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at