rs772211736
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP6
The NM_000093.5(COL5A1):c.2723C>T(p.Pro908Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,613,922 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P908S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000093.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.2723C>T | p.Pro908Leu | missense_variant | 33/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.2723C>T | p.Pro908Leu | missense_variant | 33/66 | ||
COL5A1 | XM_017014266.3 | c.2723C>T | p.Pro908Leu | missense_variant | 33/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.2723C>T | p.Pro908Leu | missense_variant | 33/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.2723C>T | p.Pro908Leu | missense_variant | 33/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250850Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135818
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461780Hom.: 0 Cov.: 39 AF XY: 0.0000110 AC XY: 8AN XY: 727174
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74318
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jan 03, 2020 | The COL5A1 c.2723C>T; p.Pro908Leu variant (rs772211736), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 409104). This variant is found on only four chromosomes (4/250850 alleles) in the Genome Aggregation Database. The proline at codon 908 is highly conserved, but computational analyses (SIFT: tolerated, PolyPhen-2: damaging) predict conflicting effects of this variant on protein structure/function. However, due to limited information, the clinical significance of the p.Pro908Leu variant is uncertain at this time. - |
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at