rs150993138
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_000093.5(COL5A1):c.2184C>A(p.Ala728=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,613,290 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A728A) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.2184C>A | p.Ala728= | synonymous_variant | 23/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.2184C>A | p.Ala728= | synonymous_variant | 23/66 | ||
COL5A1 | XM_017014266.3 | c.2184C>A | p.Ala728= | synonymous_variant | 23/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.2184C>A | p.Ala728= | synonymous_variant | 23/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.2184C>A | p.Ala728= | synonymous_variant | 23/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000524 AC: 13AN: 248272Hom.: 0 AF XY: 0.0000669 AC XY: 9AN XY: 134614
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1461140Hom.: 1 Cov.: 32 AF XY: 0.0000523 AC XY: 38AN XY: 726818
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74328
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 07, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
COL5A1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 01, 2023 | 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). - |
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at