11-68449010-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002335.4(LRP5):c.4788C>G(p.Thr1596=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000625 in 1,599,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T1596T) has been classified as Benign.
Frequency
Consequence
NM_002335.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP5 | NM_002335.4 | c.4788C>G | 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>G | p.Thr1596= | synonymous_variant | 23/23 | 1 | NM_002335.4 | P1 | |
LRP5 | ENST00000529993.5 | c.*3394C>G | 3_prime_UTR_variant, NMD_transcript_variant | 23/23 | 1 | ||||
LRP5 | ENST00000529702.1 | c.459C>G | p.Thr153= | synonymous_variant | 4/4 | 3 | |||
LRP5 | ENST00000529481.1 | n.379C>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151992Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000211 AC: 5AN: 236966Hom.: 0 AF XY: 0.0000311 AC XY: 4AN XY: 128810
GnomAD4 exome AF: 0.00000622 AC: 9AN: 1447690Hom.: 0 Cov.: 33 AF XY: 0.00000694 AC XY: 5AN XY: 720114
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151992Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74232
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at