11-121452491-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003105.6(SORL1):c.160G>C(p.Asp54His) variant causes a missense change. The variant allele was found at a frequency of 0.0000128 in 1,485,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003105.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SORL1 | NM_003105.6 | c.160G>C | p.Asp54His | missense_variant | Exon 1 of 48 | ENST00000260197.12 | NP_003096.2 | |
SORL1-AS1 | NR_183636.1 | n.293+184C>G | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SORL1 | ENST00000260197.12 | c.160G>C | p.Asp54His | missense_variant | Exon 1 of 48 | 1 | NM_003105.6 | ENSP00000260197.6 | ||
SORL1 | ENST00000532451.1 | n.112G>C | non_coding_transcript_exon_variant | Exon 1 of 15 | 1 | |||||
SORL1-AS1 | ENST00000501964.1 | n.339+184C>G | intron_variant | Intron 1 of 1 | 2 | |||||
SORL1-AS1 | ENST00000529160.1 | n.245+184C>G | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 1AN: 82904Hom.: 0 AF XY: 0.0000210 AC XY: 1AN XY: 47580
GnomAD4 exome AF: 0.0000128 AC: 17AN: 1333240Hom.: 0 Cov.: 31 AF XY: 0.0000107 AC XY: 7AN XY: 655084
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74316
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces aspartic acid, which is acidic and polar, with histidine, which is basic and polar, at codon 54 of the SORL1 protein (p.Asp54His). This variant is present in population databases (rs761865673, gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SORL1-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at