chr11-68449010-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002335.4(LRP5):c.4788C>T(p.Thr1596=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0175 in 1,599,766 control chromosomes in the GnomAD database, including 327 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T1596T) has been classified as Likely benign.
Frequency
Consequence
NM_002335.4 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 |
---|---|---|---|---|---|---|---|
LRP5 | NM_002335.4 | c.4788C>T | p.Thr1596= | synonymous_variant | 23/23 | ENST00000294304.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP5 | ENST00000294304.12 | c.4788C>T | p.Thr1596= | synonymous_variant | 23/23 | 1 | NM_002335.4 | P1 | |
LRP5 | ENST00000529993.5 | c.*3394C>T | 3_prime_UTR_variant, NMD_transcript_variant | 23/23 | 1 | ||||
LRP5 | ENST00000529702.1 | c.459C>T | p.Thr153= | synonymous_variant | 4/4 | 3 | |||
LRP5 | ENST00000529481.1 | n.379C>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0131 AC: 1996AN: 151986Hom.: 23 Cov.: 32
GnomAD3 exomes AF: 0.0153 AC: 3632AN: 236966Hom.: 46 AF XY: 0.0155 AC XY: 1994AN XY: 128810
GnomAD4 exome AF: 0.0180 AC: 26031AN: 1447664Hom.: 304 Cov.: 33 AF XY: 0.0178 AC XY: 12836AN XY: 720100
GnomAD4 genome ? AF: 0.0131 AC: 1997AN: 152102Hom.: 23 Cov.: 32 AF XY: 0.0122 AC XY: 906AN XY: 74358
ClinVar
Submissions by phenotype
not provided Benign:5
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 30, 2019 | This variant is associated with the following publications: (PMID: 15981244, 12579474, 16234968, 18721193) - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 27, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Osteogenesis imperfecta Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | May 10, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at