chr11-46871557-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002334.4(LRP4):āc.4660A>Gā(p.Ser1554Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.512 in 1,610,966 control chromosomes in the GnomAD database, including 218,679 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_002334.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRP4 | ENST00000378623.6 | c.4660A>G | p.Ser1554Gly | missense_variant | Exon 31 of 38 | 1 | NM_002334.4 | ENSP00000367888.1 | ||
LRP4 | ENST00000527656.1 | n.592A>G | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
LRP4-AS1 | ENST00000502049.3 | n.193-1517T>C | intron_variant | Intron 2 of 2 | 2 | |||||
LRP4-AS1 | ENST00000531719.5 | n.292-1517T>C | intron_variant | Intron 3 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.428 AC: 64975AN: 151950Hom.: 15955 Cov.: 31
GnomAD3 exomes AF: 0.481 AC: 118848AN: 247302Hom.: 30468 AF XY: 0.492 AC XY: 65681AN XY: 133598
GnomAD4 exome AF: 0.521 AC: 760306AN: 1458896Hom.: 202719 Cov.: 43 AF XY: 0.523 AC XY: 379363AN XY: 725626
GnomAD4 genome AF: 0.427 AC: 64974AN: 152070Hom.: 15960 Cov.: 31 AF XY: 0.429 AC XY: 31918AN XY: 74334
ClinVar
Submissions by phenotype
Cenani-Lenz syndactyly syndrome Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
- -
not provided Benign:2
This variant is associated with the following publications: (PMID: 23321396, 21121903) -
- -
Congenital myasthenic syndrome 17 Benign:1
- -
Sclerosteosis 2 Benign:1
- -
Cenani-Lenz syndactyly syndrome;C3280402:Sclerosteosis 2;C4225377:Congenital myasthenic syndrome 17 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at