16-22534154-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001395849.1(NPIPB5):c.1171C>T(p.Arg391Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R391H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001395849.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPIPB5 | NM_001395849.1 | c.1171C>T | p.Arg391Cys | missense_variant | 7/7 | ENST00000424340.7 | |
LOC105371131 | XR_007065022.1 | n.150+3324G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPIPB5 | ENST00000424340.7 | c.1171C>T | p.Arg391Cys | missense_variant | 7/7 | 1 | NM_001395849.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 18930Hom.: 0 Cov.: 5 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000338 AC: 17AN: 502780Hom.: 0 Cov.: 5 AF XY: 0.0000368 AC XY: 10AN XY: 271702
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 18930Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0AN XY: 9250
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.1171C>T (p.R391C) alteration is located in exon 7 (coding exon 7) of the NPIPB5 gene. This alteration results from a C to T substitution at nucleotide position 1171, causing the arginine (R) at amino acid position 391 to be replaced by a cysteine (C). 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