rs1800127
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_002332.3(LRP1):c.650C>T(p.Ala217Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 1,614,124 control chromosomes in the GnomAD database, including 462 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002332.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP1 | NM_002332.3 | c.650C>T | p.Ala217Val | missense_variant | 6/89 | ENST00000243077.8 | |
LRP1-AS | NR_131938.1 | n.182-216G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP1 | ENST00000243077.8 | c.650C>T | p.Ala217Val | missense_variant | 6/89 | 1 | NM_002332.3 | P1 | |
LRP1-AS | ENST00000555461.1 | n.182-216G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0179 AC: 2728AN: 152154Hom.: 38 Cov.: 32
GnomAD3 exomes AF: 0.0181 AC: 4538AN: 251278Hom.: 63 AF XY: 0.0184 AC XY: 2495AN XY: 135850
GnomAD4 exome AF: 0.0219 AC: 31961AN: 1461852Hom.: 424 Cov.: 31 AF XY: 0.0218 AC XY: 15835AN XY: 727226
GnomAD4 genome ? AF: 0.0179 AC: 2726AN: 152272Hom.: 38 Cov.: 32 AF XY: 0.0189 AC XY: 1410AN XY: 74464
ClinVar
Submissions by phenotype
LRP1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 27, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at