chr9-134806233-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000093.5(COL5A1):c.3303C>T(p.Ile1101=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000581 in 1,550,386 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. I1101I) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.3303C>T | p.Ile1101= | synonymous_variant | 42/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.3303C>T | p.Ile1101= | synonymous_variant | 42/66 | ||
COL5A1 | XM_017014266.3 | c.3303C>T | p.Ile1101= | synonymous_variant | 42/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.3303C>T | p.Ile1101= | synonymous_variant | 42/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.3303C>T | p.Ile1101= | synonymous_variant | 42/66 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152070Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000451 AC: 7AN: 155186Hom.: 0 AF XY: 0.0000489 AC XY: 4AN XY: 81820
GnomAD4 exome AF: 0.0000615 AC: 86AN: 1398316Hom.: 0 Cov.: 31 AF XY: 0.0000464 AC XY: 32AN XY: 689704
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152070Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74270
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 1 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Mar 15, 2022 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 29, 2017 | 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. - |
Fibromuscular dysplasia, multifocal Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Mar 15, 2022 | - - |
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2015 | 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | COL5A1: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at