chr2-189002351-T-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_000090.4(COL3A1):āc.2445T>Gā(p.Pro815=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000154 in 1,613,556 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000090.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL3A1 | NM_000090.4 | c.2445T>G | p.Pro815= | splice_region_variant, synonymous_variant | 35/51 | ENST00000304636.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636.9 | c.2445T>G | p.Pro815= | splice_region_variant, synonymous_variant | 35/51 | 1 | NM_000090.4 | P1 | |
COL3A1 | ENST00000450867.2 | c.2346T>G | p.Pro782= | splice_region_variant, synonymous_variant | 34/50 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000986 AC: 150AN: 152188Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000235 AC: 59AN: 251280Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135822
GnomAD4 exome AF: 0.0000678 AC: 99AN: 1461250Hom.: 0 Cov.: 30 AF XY: 0.0000674 AC XY: 49AN XY: 726972
GnomAD4 genome AF: 0.000985 AC: 150AN: 152306Hom.: 3 Cov.: 32 AF XY: 0.00148 AC XY: 110AN XY: 74474
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 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. - |
Benign, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Apr 04, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Jan 06, 2019 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 30, 2016 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 18, 2023 | - - |
Ehlers-Danlos syndrome, type 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at