chr1-7784384-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001377275.1(PER3):c.-225+8C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 150,108 control chromosomes in the GnomAD database, including 4,282 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001377275.1 splice_region, intron
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 | UniProt |
---|---|---|---|---|---|---|---|
PER3 | NM_001377275.1 | c.-225+8C>A | splice_region_variant, intron_variant | ENST00000377532.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER3 | ENST00000377532.8 | c.-225+8C>A | splice_region_variant, intron_variant | 1 | NM_001377275.1 | A2 | |||
PER3 | ENST00000377541.5 | c.-225+8C>A | splice_region_variant, intron_variant | 1 | |||||
PER3 | ENST00000614998.4 | upstream_gene_variant | 1 | A2 | |||||
PER3 | ENST00000613533.4 | upstream_gene_variant | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.221 AC: 33080AN: 149472Hom.: 4278 Cov.: 31
GnomAD4 exome AF: 0.123 AC: 64AN: 522Hom.: 3 Cov.: 0 AF XY: 0.118 AC XY: 45AN XY: 382
GnomAD4 genome AF: 0.221 AC: 33104AN: 149586Hom.: 4279 Cov.: 31 AF XY: 0.216 AC XY: 15825AN XY: 73244
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at