rs763524380
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000311.5(PRNP):c.160G>A(p.Gly54Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00041 in 1,611,090 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000311.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRNP | NM_000311.5 | c.160G>A | p.Gly54Ser | missense_variant | Exon 2 of 2 | ENST00000379440.9 | NP_000302.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRNP | ENST00000379440.9 | c.160G>A | p.Gly54Ser | missense_variant | Exon 2 of 2 | 1 | NM_000311.5 | ENSP00000368752.4 | ||
PRNP | ENST00000424424.2 | c.160G>A | p.Gly54Ser | missense_variant | Exon 2 of 2 | 1 | ENSP00000411599.2 | |||
PRNP | ENST00000430350.2 | c.160G>A | p.Gly54Ser | missense_variant | Exon 2 of 2 | 1 | ENSP00000399376.2 | |||
PRNP | ENST00000457586.2 | c.160G>A | p.Gly54Ser | missense_variant | Exon 2 of 2 | 1 | ENSP00000415284.2 |
Frequencies
GnomAD3 genomes AF: 0.000205 AC: 31AN: 151534Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000650 AC: 161AN: 247882Hom.: 1 AF XY: 0.000830 AC XY: 112AN XY: 134866
GnomAD4 exome AF: 0.000432 AC: 630AN: 1459442Hom.: 5 Cov.: 31 AF XY: 0.000577 AC XY: 419AN XY: 725850
GnomAD4 genome AF: 0.000204 AC: 31AN: 151648Hom.: 1 Cov.: 32 AF XY: 0.000270 AC XY: 20AN XY: 74134
ClinVar
Submissions by phenotype
not provided Benign:2
PRNP: BS1, BS2 -
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Inherited prion disease Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Huntington disease-like 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at