chr17-50194694-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000088.4(COL1A1):c.1461+27G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 1,558,118 control chromosomes in the GnomAD database, including 361,389 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.70 ( 37640 hom., cov: 30)
Exomes 𝑓: 0.68 ( 323749 hom. )
Consequence
COL1A1
NM_000088.4 intron
NM_000088.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.19
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 17-50194694-C-T is Benign according to our data. Variant chr17-50194694-C-T is described in ClinVar as [Benign]. Clinvar id is 674802.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.1461+27G>A | intron_variant | ENST00000225964.10 | |||
COL1A1 | XM_005257058.5 | c.1461+27G>A | intron_variant | ||||
COL1A1 | XM_005257059.5 | c.957+1620G>A | intron_variant | ||||
COL1A1 | XM_011524341.2 | c.1263+27G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.1461+27G>A | intron_variant | 1 | NM_000088.4 | P1 | |||
COL1A1 | ENST00000471344.1 | n.405+27G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.702 AC: 106514AN: 151674Hom.: 37599 Cov.: 30
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GnomAD3 exomes AF: 0.685 AC: 114975AN: 167896Hom.: 39629 AF XY: 0.678 AC XY: 60560AN XY: 89278
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GnomAD4 exome AF: 0.678 AC: 952803AN: 1406328Hom.: 323749 Cov.: 38 AF XY: 0.674 AC XY: 468359AN XY: 694668
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GnomAD4 genome ? AF: 0.702 AC: 106610AN: 151790Hom.: 37640 Cov.: 30 AF XY: 0.702 AC XY: 52082AN XY: 74208
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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 14, 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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BayesDel_noAF
Benign
Cadd
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Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at