rs1784933
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000260197.12(SORL1):c.5605-67G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 1,596,528 control chromosomes in the GnomAD database, including 683,552 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.84 ( 55544 hom., cov: 31)
Exomes 𝑓: 0.93 ( 628008 hom. )
Consequence
SORL1
ENST00000260197.12 intron
ENST00000260197.12 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.365
Genes affected
SORL1 (HGNC:11185): (sortilin related receptor 1) This gene encodes a mosaic protein that belongs to at least two families: the vacuolar protein sorting 10 (VPS10) domain-containing receptor family, and the low density lipoprotein receptor (LDLR) family. The encoded protein also contains fibronectin type III repeats and an epidermal growth factor repeat. The encoded preproprotein is proteolytically processed to generate the mature receptor, which likely plays roles in endocytosis and sorting. Mutations in this gene may be associated with Alzheimer's disease. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SORL1 | NM_003105.6 | c.5605-67G>A | intron_variant | ENST00000260197.12 | NP_003096.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SORL1 | ENST00000260197.12 | c.5605-67G>A | intron_variant | 1 | NM_003105.6 | ENSP00000260197 | P1 |
Frequencies
GnomAD3 genomes AF: 0.842 AC: 127973AN: 151966Hom.: 55523 Cov.: 31
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GnomAD4 exome AF: 0.929 AC: 1341945AN: 1444444Hom.: 628008 AF XY: 0.931 AC XY: 668956AN XY: 718736
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GnomAD4 genome AF: 0.842 AC: 128038AN: 152084Hom.: 55544 Cov.: 31 AF XY: 0.845 AC XY: 62838AN XY: 74354
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at