chr2-169205568-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004525.3(LRP2):āc.7626C>Gā(p.Arg2542=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 1,613,650 control chromosomes in the GnomAD database, including 6,434 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. R2542R) has been classified as Likely benign.
Frequency
Consequence
NM_004525.3 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 |
---|---|---|---|---|---|---|---|
LRP2 | NM_004525.3 | c.7626C>G | p.Arg2542= | synonymous_variant | 41/79 | ENST00000649046.1 | |
LRP2 | XM_011511183.4 | c.7626C>G | p.Arg2542= | synonymous_variant | 41/78 | ||
LRP2 | XM_047444340.1 | c.6702C>G | p.Arg2234= | synonymous_variant | 41/79 | ||
LRP2 | XM_011511184.3 | c.5337C>G | p.Arg1779= | synonymous_variant | 26/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP2 | ENST00000649046.1 | c.7626C>G | p.Arg2542= | synonymous_variant | 41/79 | NM_004525.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.124 AC: 18804AN: 151834Hom.: 2156 Cov.: 32
GnomAD3 exomes AF: 0.0688 AC: 17308AN: 251426Hom.: 1217 AF XY: 0.0666 AC XY: 9054AN XY: 135880
GnomAD4 exome AF: 0.0619 AC: 90493AN: 1461698Hom.: 4273 Cov.: 33 AF XY: 0.0623 AC XY: 45281AN XY: 727168
GnomAD4 genome AF: 0.124 AC: 18830AN: 151952Hom.: 2161 Cov.: 32 AF XY: 0.122 AC XY: 9061AN XY: 74286
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Donnai-Barrow syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at