rs2301643
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000089.4(COL1A2):c.1666-41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,603,114 control chromosomes in the GnomAD database, including 28,298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2416 hom., cov: 32)
Exomes 𝑓: 0.18 ( 25882 hom. )
Consequence
COL1A2
NM_000089.4 intron
NM_000089.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.60
Genes affected
COL1A2 (HGNC:2198): (collagen type I alpha 2 chain) This gene encodes the pro-alpha2 chain of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain. Type I is a fibril-forming collagen found in most connective tissues and is abundant in bone, cornea, dermis and tendon. Mutations in this gene are associated with osteogenesis imperfecta types I-IV, Ehlers-Danlos syndrome type VIIB, recessive Ehlers-Danlos syndrome Classical type, idiopathic osteoporosis, and atypical Marfan syndrome. Symptoms associated with mutations in this gene, however, tend to be less severe than mutations in the gene for the alpha1 chain of type I collagen (COL1A1) reflecting the different role of alpha2 chains in matrix integrity. Three transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 7-94414181-G-A is Benign according to our data. Variant chr7-94414181-G-A is described in ClinVar as [Benign]. Clinvar id is 674830.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A2 | NM_000089.4 | c.1666-41G>A | intron_variant | ENST00000297268.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A2 | ENST00000297268.11 | c.1666-41G>A | intron_variant | 1 | NM_000089.4 | P1 | |||
COL1A2 | ENST00000488298.5 | n.90-41G>A | intron_variant, non_coding_transcript_variant | 2 | |||||
COL1A2 | ENST00000473573.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.172 AC: 26069AN: 151968Hom.: 2412 Cov.: 32
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GnomAD3 exomes AF: 0.183 AC: 45784AN: 250562Hom.: 4986 AF XY: 0.175 AC XY: 23680AN XY: 135416
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GnomAD4 exome AF: 0.184 AC: 267454AN: 1451028Hom.: 25882 Cov.: 30 AF XY: 0.181 AC XY: 130814AN XY: 722608
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GnomAD4 genome ? AF: 0.172 AC: 26091AN: 152086Hom.: 2416 Cov.: 32 AF XY: 0.169 AC XY: 12537AN XY: 74344
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 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. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at