rs62643364
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_001271561.3(PRNP):āc.157A>Gā(p.Thr53Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000937 in 1,569,202 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001271561.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRNP | NM_000311.5 | c.246A>G | p.Gly82Gly | synonymous_variant | 2/2 | ENST00000379440.9 | NP_000302.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRNP | ENST00000379440.9 | c.246A>G | p.Gly82Gly | synonymous_variant | 2/2 | 1 | NM_000311.5 | ENSP00000368752.4 | ||
PRNP | ENST00000424424.2 | c.246A>G | p.Gly82Gly | synonymous_variant | 2/2 | 1 | ENSP00000411599.2 | |||
PRNP | ENST00000430350.2 | c.246A>G | p.Gly82Gly | synonymous_variant | 2/2 | 1 | ENSP00000399376.2 | |||
PRNP | ENST00000457586.2 | c.246A>G | p.Gly82Gly | synonymous_variant | 2/2 | 1 | ENSP00000415284.2 |
Frequencies
GnomAD3 genomes AF: 0.000229 AC: 31AN: 135606Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000145 AC: 36AN: 248842Hom.: 1 AF XY: 0.000119 AC XY: 16AN XY: 134932
GnomAD4 exome AF: 0.0000809 AC: 116AN: 1433514Hom.: 1 Cov.: 31 AF XY: 0.0000938 AC XY: 67AN XY: 714164
GnomAD4 genome AF: 0.000228 AC: 31AN: 135688Hom.: 0 Cov.: 31 AF XY: 0.000210 AC XY: 14AN XY: 66556
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Inherited prion disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Huntington disease-like 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 21, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at