16-14951777-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006985.4(NPIPA1):āc.805T>Cā(p.Cys269Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00199 in 120,914 control chromosomes in the GnomAD database, including 4 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 Likely benign (ā ).
Frequency
Consequence
NM_006985.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPIPA1 | NM_006985.4 | c.805T>C | p.Cys269Arg | missense_variant | 8/8 | ENST00000328085.10 | |
PKD1P3-NPIPA1 | NR_146231.1 | n.7082T>C | non_coding_transcript_exon_variant | 39/39 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPIPA1 | ENST00000328085.10 | c.805T>C | p.Cys269Arg | missense_variant | 8/8 | 1 | NM_006985.4 | P1 | |
NPIPA1 | ENST00000472413.5 | n.5062T>C | non_coding_transcript_exon_variant | 28/28 | 2 | ||||
NPIPA1 | ENST00000541836.5 | n.2650T>C | non_coding_transcript_exon_variant | 20/20 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00199 AC: 240AN: 120846Hom.: 4 Cov.: 22
GnomAD3 exomes AF: 0.00183 AC: 378AN: 206398Hom.: 22 AF XY: 0.00185 AC XY: 208AN XY: 112588
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0237 AC: 29724AN: 1254738Hom.: 168 Cov.: 33 AF XY: 0.0241 AC XY: 15079AN XY: 625320
GnomAD4 genome AF: 0.00199 AC: 241AN: 120914Hom.: 4 Cov.: 22 AF XY: 0.00197 AC XY: 115AN XY: 58340
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | NPIPA1: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at