17-50184475-CAAAAAAA-CAAAAAAAAA
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_000088.4(COL1A1):c.*1025_*1026dupTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00477 in 121,444 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00078 ( 1 hom., cov: 26)
Exomes 𝑓: 0.011 ( 0 hom. )
Consequence
COL1A1
NM_000088.4 3_prime_UTR
NM_000088.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.156
Genes affected
COL1A1 (HGNC:2197): (collagen type I alpha 1 chain) This gene encodes the pro-alpha1 chains 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 VIIA, Ehlers-Danlos syndrome Classical type, Caffey Disease and idiopathic osteoporosis. Reciprocal translocations between chromosomes 17 and 22, where this gene and the gene for platelet-derived growth factor beta are located, are associated with a particular type of skin tumor called dermatofibrosarcoma protuberans, resulting from unregulated expression of the growth factor. Two 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 -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.0108 (522/48364) while in subpopulation AFR AF= 0.0175 (38/2168). AF 95% confidence interval is 0.0131. There are 0 homozygotes in gnomad4_exome. There are 247 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 57 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.*1025_*1026dupTT | 3_prime_UTR_variant | Exon 51 of 51 | ENST00000225964.10 | NP_000079.2 | ||
COL1A1 | XM_011524341.2 | c.*1025_*1026dupTT | 3_prime_UTR_variant | Exon 48 of 48 | XP_011522643.1 | |||
COL1A1 | XM_005257058.5 | c.*1025_*1026dupTT | 3_prime_UTR_variant | Exon 49 of 49 | XP_005257115.2 | |||
COL1A1 | XM_005257059.5 | c.*1025_*1026dupTT | 3_prime_UTR_variant | Exon 38 of 38 | XP_005257116.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000780 AC: 57AN: 73080Hom.: 1 Cov.: 26
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GnomAD4 exome AF: 0.0108 AC: 522AN: 48364Hom.: 0 Cov.: 0 AF XY: 0.0110 AC XY: 247AN XY: 22440
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GnomAD4 genome AF: 0.000780 AC: 57AN: 73080Hom.: 1 Cov.: 26 AF XY: 0.000979 AC XY: 34AN XY: 34744
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at