rs41264443
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000304636.9(COL3A1):c.3039+16T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000786 in 1,591,614 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00061 ( 2 hom. )
Consequence
COL3A1
ENST00000304636.9 intron
ENST00000304636.9 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.974
Genes affected
COL3A1 (HGNC:2201): (collagen type III alpha 1 chain) This gene encodes the pro-alpha1 chains of type III collagen, a fibrillar collagen that is found in extensible connective tissues such as skin, lung, uterus, intestine and the vascular system, frequently in association with type I collagen. Mutations in this gene are associated with Ehlers-Danlos syndrome type IV, and with aortic and arterial aneurysms. [provided by R. Dalgleish, Feb 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 2-189005473-T-G is Benign according to our data. Variant chr2-189005473-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 136855.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-189005473-T-G is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00244 (372/152342) while in subpopulation AFR AF= 0.00726 (302/41584). AF 95% confidence interval is 0.00659. There are 0 homozygotes in gnomad4. There are 167 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 2 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL3A1 | NM_000090.4 | c.3039+16T>G | intron_variant | ENST00000304636.9 | NP_000081.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636.9 | c.3039+16T>G | intron_variant | 1 | NM_000090.4 | ENSP00000304408 | P1 | |||
COL3A1 | ENST00000450867.2 | c.2940+16T>G | intron_variant | 1 | ENSP00000415346 |
Frequencies
GnomAD3 genomes AF: 0.00244 AC: 371AN: 152224Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00109 AC: 275AN: 251170Hom.: 0 AF XY: 0.000847 AC XY: 115AN XY: 135780
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GnomAD4 exome AF: 0.000611 AC: 879AN: 1439272Hom.: 2 Cov.: 26 AF XY: 0.000582 AC XY: 418AN XY: 717678
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GnomAD4 genome AF: 0.00244 AC: 372AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.00224 AC XY: 167AN XY: 74496
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 02, 2014 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 05, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 14, 2023 | - - |
Ehlers-Danlos syndrome, type 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 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