2-188974482-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000090.4(COL3A1):c.-8A>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,606,782 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 (★).
Frequency
Consequence
NM_000090.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL3A1 | NM_000090.4 | c.-8A>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 51 | ENST00000304636.9 | NP_000081.2 | ||
COL3A1 | NM_000090.4 | c.-8A>G | 5_prime_UTR_variant | Exon 1 of 51 | ENST00000304636.9 | NP_000081.2 | ||
LOC105373791 | XR_007087614.1 | n.110-4003T>C | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636 | c.-8A>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 51 | 1 | NM_000090.4 | ENSP00000304408.4 | |||
COL3A1 | ENST00000304636 | c.-8A>G | 5_prime_UTR_variant | Exon 1 of 51 | 1 | NM_000090.4 | ENSP00000304408.4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1454702Hom.: 0 Cov.: 29 AF XY: 0.00000552 AC XY: 4AN XY: 724186
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74282
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, type 4 Uncertain:1
This variant is located in the 5' untranslated region of the COL3A1 gene. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with COL3A1-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at