rs200620805
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_000088.4(COL1A1):c.2508C>T(p.Gly836=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,610,258 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G836G) has been classified as Likely benign.
Frequency
Consequence
NM_000088.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.2508C>T | p.Gly836= | synonymous_variant | 36/51 | ENST00000225964.10 | |
COL1A1 | XM_011524341.2 | c.2310C>T | p.Gly770= | synonymous_variant | 33/48 | ||
COL1A1 | XM_005257058.5 | c.2508C>T | p.Gly836= | synonymous_variant | 36/49 | ||
COL1A1 | XM_005257059.5 | c.1590C>T | p.Gly530= | synonymous_variant | 23/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.2508C>T | p.Gly836= | synonymous_variant | 36/51 | 1 | NM_000088.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000605 AC: 9AN: 148720Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250622Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135722
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461410Hom.: 1 Cov.: 37 AF XY: 0.0000248 AC XY: 18AN XY: 726980
GnomAD4 genome AF: 0.0000605 AC: 9AN: 148848Hom.: 0 Cov.: 33 AF XY: 0.0000275 AC XY: 2AN XY: 72764
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 19, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 27, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2021 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2020 | 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. - |
Osteogenesis imperfecta type I Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at