11-68312693-GC-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_002335.4(LRP5):c.-19delC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00852 in 993,782 control chromosomes in the GnomAD database, including 45 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002335.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRP5 | ENST00000294304 | c.-19delC | 5_prime_UTR_variant | Exon 1 of 23 | 1 | NM_002335.4 | ENSP00000294304.6 | |||
LRP5 | ENST00000529993.5 | n.-19delC | non_coding_transcript_exon_variant | Exon 1 of 23 | 1 | ENSP00000436652.1 | ||||
LRP5 | ENST00000529993.5 | n.-19delC | 5_prime_UTR_variant | Exon 1 of 23 | 1 | ENSP00000436652.1 |
Frequencies
GnomAD3 genomes AF: 0.00668 AC: 966AN: 144672Hom.: 5 Cov.: 30
GnomAD3 exomes AF: 0.00220 AC: 2AN: 908Hom.: 0 AF XY: 0.00187 AC XY: 1AN XY: 534
GnomAD4 exome AF: 0.00883 AC: 7498AN: 848994Hom.: 40 Cov.: 16 AF XY: 0.00867 AC XY: 3447AN XY: 397760
GnomAD4 genome AF: 0.00667 AC: 966AN: 144788Hom.: 5 Cov.: 30 AF XY: 0.00591 AC XY: 417AN XY: 70508
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
LRP5: BS2 -
- -
See Variant Classification Assertion Criteria. -
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at