chr3-99795506-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_020351.4(COL8A1):c.1605C>T(p.Pro535=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00484 in 1,588,242 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0050 ( 19 hom. )
Consequence
COL8A1
NM_020351.4 synonymous
NM_020351.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.95
Genes affected
COL8A1 (HGNC:2215): (collagen type VIII alpha 1 chain) This gene encodes one of the two alpha chains of type VIII collagen. The gene product is a short chain collagen and a major component of the basement membrane of the corneal endothelium. The type VIII collagen fibril can be either a homo- or a heterotrimer. Alternatively spliced transcript variants encoding the same protein have been observed. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 3-99795506-C-T is Benign according to our data. Variant chr3-99795506-C-T is described in ClinVar as [Benign]. Clinvar id is 784470.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.95 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL8A1 | NM_020351.4 | c.1605C>T | p.Pro535= | synonymous_variant | 4/4 | ENST00000652472.1 | |
COL8A1 | NM_001850.5 | c.1605C>T | p.Pro535= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL8A1 | ENST00000652472.1 | c.1605C>T | p.Pro535= | synonymous_variant | 4/4 | NM_020351.4 | P1 | ||
COL8A1 | ENST00000261037.7 | c.1605C>T | p.Pro535= | synonymous_variant | 5/5 | 1 | P1 | ||
COL8A1 | ENST00000273342.8 | c.1605C>T | p.Pro535= | synonymous_variant | 4/4 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00369 AC: 559AN: 151580Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00380 AC: 794AN: 209012Hom.: 4 AF XY: 0.00380 AC XY: 433AN XY: 114048
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GnomAD4 exome AF: 0.00496 AC: 7123AN: 1436544Hom.: 19 Cov.: 32 AF XY: 0.00481 AC XY: 3429AN XY: 712330
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GnomAD4 genome AF: 0.00368 AC: 559AN: 151698Hom.: 3 Cov.: 32 AF XY: 0.00374 AC XY: 277AN XY: 74120
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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 | Invitae | Jun 15, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at