rs3736228
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_002335.4(LRP5):c.3989C>T(p.Ala1330Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 1,611,778 control chromosomes in the GnomAD database, including 17,351 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A1330A) has been classified as Likely benign.
Frequency
Consequence
NM_002335.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP5 | NM_002335.4 | c.3989C>T | p.Ala1330Val | missense_variant | 18/23 | ENST00000294304.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP5 | ENST00000294304.12 | c.3989C>T | p.Ala1330Val | missense_variant | 18/23 | 1 | NM_002335.4 | P1 | |
LRP5 | ENST00000529993.5 | c.*2595C>T | 3_prime_UTR_variant, NMD_transcript_variant | 18/23 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.111 AC: 16841AN: 152168Hom.: 1184 Cov.: 33
GnomAD3 exomes AF: 0.134 AC: 32608AN: 243164Hom.: 2508 AF XY: 0.132 AC XY: 17593AN XY: 132822
GnomAD4 exome AF: 0.144 AC: 209942AN: 1459492Hom.: 16169 Cov.: 33 AF XY: 0.143 AC XY: 104076AN XY: 726148
GnomAD4 genome ? AF: 0.111 AC: 16846AN: 152286Hom.: 1182 Cov.: 33 AF XY: 0.108 AC XY: 8013AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | This variant is associated with the following publications: (PMID: 33302760, 25580429, 30283887, 16355283, 18026682, 16713434, 18455228, 18349089, 17955262, 19571442, 21432225, 18058054, 22511589, 21116122) - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 24, 2018 | - - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 14, 2015 | - - |
Osteogenesis imperfecta Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jul 18, 2022 | - - |
Increased bone mineral density Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Mar 31, 2021 | - - |
Osteoporosis with pseudoglioma Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at