rs142352627
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_000089.4(COL1A2):c.2904C>G(p.Pro968=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,612,280 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 Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. P968P) has been classified as Likely benign.
Frequency
Consequence
NM_000089.4 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 |
---|---|---|---|---|---|---|---|
COL1A2 | NM_000089.4 | c.2904C>G | p.Pro968= | synonymous_variant | 44/52 | ENST00000297268.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A2 | ENST00000297268.11 | c.2904C>G | p.Pro968= | synonymous_variant | 44/52 | 1 | NM_000089.4 | P1 | |
COL1A2 | ENST00000478215.1 | n.463C>G | non_coding_transcript_exon_variant | 2/4 | 3 | ||||
COL1A2 | ENST00000481570.5 | n.2877C>G | non_coding_transcript_exon_variant | 3/8 | 2 | ||||
COL1A2 | ENST00000469732.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246316Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133108
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460176Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726246
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 02, 2018 | - - |
Osteogenesis imperfecta type I;C0268335:Ehlers-Danlos syndrome, classic type, 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 596006). This variant has not been reported in the literature in individuals affected with COL1A2-related conditions. This variant is present in population databases (rs142352627, gnomAD 0.007%). This sequence change affects codon 968 of the COL1A2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the COL1A2 protein. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at