rs41272029
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001844.5(COL2A1):c.2673C>T(p.Gly891=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000386 in 1,554,832 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. G891G) has been classified as Benign.
Frequency
Consequence
NM_001844.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL2A1 | NM_001844.5 | c.2673C>T | p.Gly891= | synonymous_variant | 40/54 | ENST00000380518.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.2673C>T | p.Gly891= | synonymous_variant | 40/54 | 1 | NM_001844.5 | P1 | |
COL2A1 | ENST00000337299.7 | c.2466C>T | p.Gly822= | synonymous_variant | 39/53 | 1 | |||
COL2A1 | ENST00000493991.5 | n.1759C>T | non_coding_transcript_exon_variant | 23/37 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000621 AC: 1AN: 161096Hom.: 0 AF XY: 0.0000117 AC XY: 1AN XY: 85280
GnomAD4 exome AF: 0.00000356 AC: 5AN: 1402746Hom.: 0 Cov.: 32 AF XY: 0.00000722 AC XY: 5AN XY: 692380
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74276
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at