rs35017779
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_000088.4(COL1A1):c.2175C>T(p.Gly725=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00194 in 1,614,030 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.010 ( 34 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 33 hom. )
Consequence
COL1A1
NM_000088.4 synonymous
NM_000088.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.336
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 -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 17-50191443-G-A is Benign according to our data. Variant chr17-50191443-G-A is described in ClinVar as [Benign]. Clinvar id is 456746.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-50191443-G-A is described in Lovd as [Benign]. Variant chr17-50191443-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.336 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0103 (1575/152224) while in subpopulation AFR AF= 0.0349 (1449/41520). AF 95% confidence interval is 0.0334. There are 34 homozygotes in gnomad4. There are 760 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1575 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.2175C>T | p.Gly725= | synonymous_variant | 32/51 | ENST00000225964.10 | |
COL1A1 | XM_011524341.2 | c.1977C>T | p.Gly659= | synonymous_variant | 29/48 | ||
COL1A1 | XM_005257058.5 | c.2175C>T | p.Gly725= | synonymous_variant | 32/49 | ||
COL1A1 | XM_005257059.5 | c.1257C>T | p.Gly419= | synonymous_variant | 19/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.2175C>T | p.Gly725= | synonymous_variant | 32/51 | 1 | NM_000088.4 | P1 | |
COL1A1 | ENST00000476387.1 | n.524C>T | non_coding_transcript_exon_variant | 8/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0103 AC: 1574AN: 152106Hom.: 35 Cov.: 33
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GnomAD3 exomes AF: 0.00277 AC: 696AN: 251402Hom.: 23 AF XY: 0.00201 AC XY: 273AN XY: 135896
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GnomAD4 exome AF: 0.00106 AC: 1555AN: 1461806Hom.: 33 Cov.: 32 AF XY: 0.000886 AC XY: 644AN XY: 727218
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GnomAD4 genome ? AF: 0.0103 AC: 1575AN: 152224Hom.: 34 Cov.: 33 AF XY: 0.0102 AC XY: 760AN XY: 74418
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 26, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | May 02, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 28, 2017 | 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. - |
Osteogenesis imperfecta Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jan 08, 2021 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2019 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Osteogenesis imperfecta type I Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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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