rs754948598
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP6BS2
The NM_000093.5(COL5A1):c.1402G>A(p.Glu468Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000204 in 1,613,930 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E468Q) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 missense
Scores
Clinical Significance
Conservation
Publications
- Ehlers-Danlos syndromeInheritance: AD Classification: DEFINITIVE Submitted by: G2P
- Ehlers-Danlos syndrome, classic typeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, Ambry Genetics, PanelApp Australia, Genomics England PanelApp
- Ehlers-Danlos syndrome, classic type, 1Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- arterial disorderInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000093.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| COL5A1 | NM_000093.5 | MANE Select | c.1402G>A | p.Glu468Lys | missense | Exon 10 of 66 | NP_000084.3 | ||
| COL5A1 | NM_001278074.1 | c.1402G>A | p.Glu468Lys | missense | Exon 10 of 66 | NP_001265003.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| COL5A1 | ENST00000371817.8 | TSL:1 MANE Select | c.1402G>A | p.Glu468Lys | missense | Exon 10 of 66 | ENSP00000360882.3 | ||
| COL5A1 | ENST00000371820.4 | TSL:2 | c.1402G>A | p.Glu468Lys | missense | Exon 10 of 66 | ENSP00000360885.4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000279 AC: 7AN: 251284 AF XY: 0.0000221 show subpopulations
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461714Hom.: 1 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727174 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74346 show subpopulations
ClinVar
ClinVar submissions as Germline
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at