rs724159967
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_002335.4(LRP5):c.4587G>A(p.Arg1529=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002335.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP5 | NM_002335.4 | c.4587G>A | p.Arg1529= | splice_region_variant, synonymous_variant | 23/23 | ENST00000294304.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP5 | ENST00000294304.12 | c.4587G>A | p.Arg1529= | splice_region_variant, synonymous_variant | 23/23 | 1 | NM_002335.4 | P1 | |
LRP5 | ENST00000529993.5 | c.*3193G>A | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 23/23 | 1 | ||||
LRP5 | ENST00000529702.1 | c.258G>A | p.Arg86= | splice_region_variant, synonymous_variant | 4/4 | 3 | |||
LRP5 | ENST00000529481.1 | n.178G>A | splice_region_variant, non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000413 AC: 1AN: 242126Hom.: 0 AF XY: 0.00000759 AC XY: 1AN XY: 131786
GnomAD4 exome Cov.: 33
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at