rs116306908
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_003383.5(VLDLR):āc.982A>Gā(p.Ser328Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000408 in 1,614,184 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S328S) has been classified as Likely benign.
Frequency
Consequence
NM_003383.5 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 |
---|---|---|---|---|---|---|---|
VLDLR | NM_003383.5 | c.982A>G | p.Ser328Gly | missense_variant | 7/19 | ENST00000382100.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VLDLR | ENST00000382100.8 | c.982A>G | p.Ser328Gly | missense_variant | 7/19 | 1 | NM_003383.5 |
Frequencies
GnomAD3 genomes ? AF: 0.00223 AC: 340AN: 152178Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000494 AC: 124AN: 251092Hom.: 0 AF XY: 0.000398 AC XY: 54AN XY: 135700
GnomAD4 exome AF: 0.000218 AC: 318AN: 1461888Hom.: 2 Cov.: 31 AF XY: 0.000204 AC XY: 148AN XY: 727244
GnomAD4 genome ? AF: 0.00224 AC: 341AN: 152296Hom.: 1 Cov.: 32 AF XY: 0.00207 AC XY: 154AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:2Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 17, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 14, 2016 | A variant of uncertain significance has been identified in the VLDLR gene. The S328G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The S328G variant is observed in 71/10,354 (0.7%) alleles from individuals of African background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The S328G variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 29, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
VLDLR-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 01, 2021 | This variant is classified as likely 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