11-68312730-C-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_002335.4(LRP5):c.16C>A(p.Pro6Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000662 in 1,052,528 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00293 AC: 425AN: 144936Hom.: 5 Cov.: 31
GnomAD3 exomes AF: 0.00872 AC: 125AN: 14342Hom.: 5 AF XY: 0.00634 AC XY: 55AN XY: 8672
GnomAD4 exome AF: 0.000301 AC: 273AN: 907488Hom.: 9 Cov.: 28 AF XY: 0.000259 AC XY: 112AN XY: 432226
GnomAD4 genome AF: 0.00292 AC: 424AN: 145040Hom.: 5 Cov.: 31 AF XY: 0.00320 AC XY: 226AN XY: 70618
ClinVar
Submissions by phenotype
not provided Benign:4
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Osteogenesis imperfecta Benign:1
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at