rs3087476
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004153.4(ORC1):c.1115C>T(p.Ala372Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0165 in 1,613,960 control chromosomes in the GnomAD database, including 250 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004153.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ORC1 | NM_004153.4 | c.1115C>T | p.Ala372Val | missense_variant | 7/17 | ENST00000371568.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ORC1 | ENST00000371568.8 | c.1115C>T | p.Ala372Val | missense_variant | 7/17 | 1 | NM_004153.4 | P1 | |
ORC1 | ENST00000371566.1 | c.1115C>T | p.Ala372Val | missense_variant | 7/17 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0136 AC: 2064AN: 152178Hom.: 21 Cov.: 32
GnomAD3 exomes AF: 0.0151 AC: 3797AN: 251474Hom.: 37 AF XY: 0.0150 AC XY: 2037AN XY: 135910
GnomAD4 exome AF: 0.0168 AC: 24506AN: 1461666Hom.: 229 Cov.: 31 AF XY: 0.0166 AC XY: 12069AN XY: 727154
GnomAD4 genome ? AF: 0.0136 AC: 2067AN: 152294Hom.: 21 Cov.: 32 AF XY: 0.0131 AC XY: 973AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 06, 2015 | - - |
Meier-Gorlin syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at