17-8143460-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002616.3(PER1):āc.2878G>Cā(p.Ala960Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000312 in 1,600,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_002616.3 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 |
---|---|---|---|---|---|---|---|
PER1 | NM_002616.3 | c.2878G>C | p.Ala960Pro | missense_variant | 19/23 | ENST00000317276.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER1 | ENST00000317276.9 | c.2878G>C | p.Ala960Pro | missense_variant | 19/23 | 1 | NM_002616.3 | P1 | |
PER1 | ENST00000581082.5 | c.2809G>C | p.Ala937Pro | missense_variant | 18/22 | 5 | |||
PER1 | ENST00000578089.1 | n.811G>C | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
PER1 | ENST00000582719.5 | c.2462-625G>C | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151396Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000126 AC: 3AN: 238226Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 128920
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1449288Hom.: 0 Cov.: 35 AF XY: 0.00000278 AC XY: 2AN XY: 720228
GnomAD4 genome AF: 0.00000660 AC: 1AN: 151514Hom.: 0 Cov.: 29 AF XY: 0.0000135 AC XY: 1AN XY: 74056
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at