rs35998480
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022817.3(PER2):c.2846T>A(p.Phe949Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000196 in 1,593,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F949L) has been classified as Uncertain significance.
Frequency
Consequence
NM_022817.3 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 |
---|---|---|---|---|---|---|---|
PER2 | NM_022817.3 | c.2846T>A | p.Phe949Tyr | missense_variant | 19/23 | ENST00000254657.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER2 | ENST00000254657.8 | c.2846T>A | p.Phe949Tyr | missense_variant | 19/23 | 1 | NM_022817.3 | P1 | |
ENST00000456601.1 | n.1525-1011A>T | intron_variant, non_coding_transcript_variant | 2 | ||||||
PER2 | ENST00000707129.1 | c.2846T>A | p.Phe949Tyr | missense_variant | 19/23 | P1 | |||
PER2 | ENST00000707130.1 | c.2846T>A | p.Phe949Tyr | missense_variant | 19/23 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00102 AC: 154AN: 151364Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000263 AC: 63AN: 239728Hom.: 0 AF XY: 0.000171 AC XY: 22AN XY: 128906
GnomAD4 exome AF: 0.000109 AC: 157AN: 1442104Hom.: 0 Cov.: 34 AF XY: 0.000109 AC XY: 78AN XY: 714026
GnomAD4 genome AF: 0.00102 AC: 155AN: 151482Hom.: 0 Cov.: 33 AF XY: 0.000852 AC XY: 63AN XY: 73934
ClinVar
Submissions by phenotype
PER2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 25, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at