chr2-188974480-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_000090.4(COL3A1):c.-10A>G variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.00000373 in 1,610,450 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
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636 | c.-10A>G | 5_prime_UTR_variant | Exon 1 of 51 | 1 | NM_000090.4 | ENSP00000304408.4 | |||
COL3A1 | ENST00000450867 | c.-10A>G | 5_prime_UTR_variant | Exon 1 of 50 | 1 | ENSP00000415346.2 | ||||
COL3A1 | ENST00000470167.1 | n.87A>G | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251292Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135812
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458354Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 725790
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74286
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection 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 cardiovascular disorders in the literature. This variant has been identified in 4/251292 chromosomes 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. -
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 cardiovascular disorders in the literature. This variant has been identified in 4/251292 chromosomes 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