rs576742644
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS2
The NM_000093.5(COL5A1):c.983G>A(p.Gly328Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,614,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000093.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.983G>A | p.Gly328Glu | missense_variant | 7/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.983G>A | p.Gly328Glu | missense_variant | 7/66 | ||
COL5A1 | XM_017014266.3 | c.983G>A | p.Gly328Glu | missense_variant | 7/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.983G>A | p.Gly328Glu | missense_variant | 7/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.983G>A | p.Gly328Glu | missense_variant | 7/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152236Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251416Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135884
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461850Hom.: 0 Cov.: 35 AF XY: 0.0000743 AC XY: 54AN XY: 727228
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152354Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74504
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 11, 2019 | Reported in conjunction with several other variants in a female child with idiopathic alveolar hypoplasia, pulmonary hypertension, and a family history of consanguinity (Omoyinmi et al., 2017); Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID# 529272; Landrum et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Not located in the triple helical region, where the majority of pathogenic missense variants occur (Symoens et al., 2012; Stenson et al., 2014); This variant is associated with the following publications: (PMID: 28750028) - |
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at