rs28763878
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000090.4(COL3A1):c.2661+22T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 1,613,042 control chromosomes in the GnomAD database, including 1,109 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.023 ( 44 hom., cov: 32)
Exomes 𝑓: 0.035 ( 1065 hom. )
Consequence
COL3A1
NM_000090.4 intron
NM_000090.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.06
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 2-189003809-T-A is Benign according to our data. Variant chr2-189003809-T-A is described in ClinVar as [Benign]. Clinvar id is 254965.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189003809-T-A is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0227 (3462/152304) while in subpopulation NFE AF= 0.0371 (2522/68022). AF 95% confidence interval is 0.0359. There are 44 homozygotes in gnomad4. There are 1592 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 44 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL3A1 | NM_000090.4 | c.2661+22T>A | intron_variant | ENST00000304636.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636.9 | c.2661+22T>A | intron_variant | 1 | NM_000090.4 | P1 | |||
COL3A1 | ENST00000450867.2 | c.2562+22T>A | intron_variant | 1 | |||||
COL3A1 | ENST00000467886.1 | n.118T>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0227 AC: 3462AN: 152186Hom.: 44 Cov.: 32
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GnomAD3 exomes AF: 0.0234 AC: 5888AN: 251344Hom.: 110 AF XY: 0.0233 AC XY: 3159AN XY: 135834
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GnomAD4 exome AF: 0.0348 AC: 50883AN: 1460738Hom.: 1065 Cov.: 31 AF XY: 0.0339 AC XY: 24658AN XY: 726796
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GnomAD4 genome ? AF: 0.0227 AC: 3462AN: 152304Hom.: 44 Cov.: 32 AF XY: 0.0214 AC XY: 1592AN XY: 74476
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
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