rs4988319
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002335.4(LRP5):c.1412+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,610,102 control chromosomes in the GnomAD database, including 21,382 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002335.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRP5 | NM_002335.4 | c.1412+8G>A | splice_region_variant, intron_variant | ENST00000294304.12 | NP_002326.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRP5 | ENST00000294304.12 | c.1412+8G>A | splice_region_variant, intron_variant | 1 | NM_002335.4 | ENSP00000294304.6 | ||||
LRP5 | ENST00000529993.5 | n.1412+8G>A | splice_region_variant, intron_variant | 1 | ENSP00000436652.1 |
Frequencies
GnomAD3 genomes AF: 0.147 AC: 22391AN: 152170Hom.: 1719 Cov.: 33
GnomAD3 exomes AF: 0.136 AC: 33041AN: 242994Hom.: 2391 AF XY: 0.133 AC XY: 17599AN XY: 132474
GnomAD4 exome AF: 0.160 AC: 232867AN: 1457814Hom.: 19662 Cov.: 35 AF XY: 0.157 AC XY: 113760AN XY: 724958
GnomAD4 genome AF: 0.147 AC: 22411AN: 152288Hom.: 1720 Cov.: 33 AF XY: 0.141 AC XY: 10533AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 24, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at