chr10-116547408-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000936.4(PNLIP):c.161G>A(p.Arg54His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,720 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R54G) has been classified as Uncertain significance.
Frequency
Consequence
NM_000936.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNLIP | NM_000936.4 | c.161G>A | p.Arg54His | missense_variant | 3/13 | ENST00000369221.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNLIP | ENST00000369221.2 | c.161G>A | p.Arg54His | missense_variant | 3/13 | 1 | NM_000936.4 | P1 | |
PNLIP | ENST00000470562.1 | n.161G>A | non_coding_transcript_exon_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152020Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251374Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135846
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461700Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727162
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152020Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2021 | The c.161G>A (p.R54H) alteration is located in exon 3 (coding exon 2) of the PNLIP gene. This alteration results from a G to A substitution at nucleotide position 161, causing the arginine (R) at amino acid position 54 to be replaced by a histidine (H). 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