rs141815296
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_080680.3(COL11A2):c.1875C>T(p.Gly625=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000357 in 1,612,752 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_080680.3 splice_region, 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 |
---|---|---|---|---|---|---|---|
COL11A2 | NM_080680.3 | c.1875C>T | p.Gly625= | splice_region_variant, synonymous_variant | 22/66 | ENST00000341947.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL11A2 | ENST00000341947.7 | c.1875C>T | p.Gly625= | splice_region_variant, synonymous_variant | 22/66 | 5 | NM_080680.3 | P4 | |
COL11A2 | ENST00000374708.8 | c.1617C>T | p.Gly539= | splice_region_variant, synonymous_variant | 20/64 | 5 | A1 | ||
COL11A2 | ENST00000361917.6 | c.450C>T | p.Gly150= | splice_region_variant, synonymous_variant | 9/24 | 5 | |||
COL11A2 | ENST00000477772.1 | n.94C>T | splice_region_variant, non_coding_transcript_exon_variant | 2/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000290 AC: 44AN: 151920Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00152 AC: 374AN: 246362Hom.: 2 AF XY: 0.00124 AC XY: 166AN XY: 134348
GnomAD4 exome AF: 0.000364 AC: 532AN: 1460714Hom.: 1 Cov.: 33 AF XY: 0.000333 AC XY: 242AN XY: 726678
GnomAD4 genome ? AF: 0.000289 AC: 44AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74306
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 05, 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. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 26, 2015 | p.Gly625Gly in exon 22 of COL11A2: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wi thin the splice consensus sequence, and has been identified in 1.4% (154/11388) of Latino chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.bro adinstitute.org; dbSNP rs141815296). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at