rs72897663
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_002334.4(LRP4):āc.1501A>Cā(p.Asn501His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 1,613,212 control chromosomes in the GnomAD database, including 1,459 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. N501N) has been classified as Likely benign.
Frequency
Consequence
NM_002334.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP4 | NM_002334.4 | c.1501A>C | p.Asn501His | missense_variant | 12/38 | ENST00000378623.6 | |
LRP4 | XM_017017734.2 | c.1501A>C | p.Asn501His | missense_variant | 12/39 | ||
LRP4 | XM_011520103.3 | c.697A>C | p.Asn233His | missense_variant | 6/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP4 | ENST00000378623.6 | c.1501A>C | p.Asn501His | missense_variant | 12/38 | 1 | NM_002334.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0316 AC: 4808AN: 152182Hom.: 129 Cov.: 32
GnomAD3 exomes AF: 0.0345 AC: 8591AN: 249058Hom.: 186 AF XY: 0.0351 AC XY: 4724AN XY: 134636
GnomAD4 exome AF: 0.0397 AC: 57935AN: 1460912Hom.: 1330 Cov.: 33 AF XY: 0.0392 AC XY: 28494AN XY: 726676
GnomAD4 genome ? AF: 0.0315 AC: 4803AN: 152300Hom.: 129 Cov.: 32 AF XY: 0.0317 AC XY: 2364AN XY: 74476
ClinVar
Submissions by phenotype
Cenani-Lenz syndactyly syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Cenani-Lenz syndactyly syndrome;C3280402:Sclerosteosis 2;C4225377:Congenital myasthenic syndrome 17 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at