NM_002334.4:c.5165T>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002334.4(LRP4):c.5165T>A(p.Leu1722His) variant causes a missense change. The variant allele was found at a frequency of 0.0206 in 1,611,148 control chromosomes in the GnomAD database, including 438 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002334.4 missense
Scores
Clinical Significance
Conservation
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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.5165T>A | p.Leu1722His | missense_variant | Exon 36 of 38 | 1 | NM_002334.4 | ENSP00000367888.1 | ||
LRP4-AS1 | ENST00000502049.3 | n.193-8548A>T | intron_variant | Intron 2 of 2 | 2 | |||||
LRP4-AS1 | ENST00000531719.5 | n.292-8548A>T | intron_variant | Intron 3 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0178 AC: 2713AN: 152232Hom.: 50 Cov.: 32
GnomAD3 exomes AF: 0.0194 AC: 4875AN: 250854Hom.: 77 AF XY: 0.0196 AC XY: 2656AN XY: 135570
GnomAD4 exome AF: 0.0209 AC: 30531AN: 1458798Hom.: 388 Cov.: 29 AF XY: 0.0204 AC XY: 14826AN XY: 726026
GnomAD4 genome AF: 0.0178 AC: 2711AN: 152350Hom.: 50 Cov.: 32 AF XY: 0.0183 AC XY: 1366AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:4
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Cenani-Lenz syndactyly syndrome Benign:1
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at