chr2-219570312-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015311.3(OBSL1):āc.921T>Cā(p.Leu307=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 1,611,404 control chromosomes in the GnomAD database, including 634,715 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L307L?) has been classified as Likely pathogenic.
Frequency
Consequence
NM_015311.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OBSL1 | NM_015311.3 | c.921T>C | p.Leu307= | synonymous_variant | 1/21 | ENST00000404537.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OBSL1 | ENST00000404537.6 | c.921T>C | p.Leu307= | synonymous_variant | 1/21 | 1 | NM_015311.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.814 AC: 123845AN: 152132Hom.: 51711 Cov.: 35
GnomAD3 exomes AF: 0.865 AC: 208361AN: 240848Hom.: 90925 AF XY: 0.870 AC XY: 114187AN XY: 131302
GnomAD4 exome AF: 0.892 AC: 1301872AN: 1459154Hom.: 582974 Cov.: 64 AF XY: 0.891 AC XY: 646818AN XY: 725614
GnomAD4 genome AF: 0.814 AC: 123927AN: 152250Hom.: 51741 Cov.: 35 AF XY: 0.815 AC XY: 60689AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 01, 2016 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
3M syndrome 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at