chr6-56059169-G-A
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_030820.4(COL21A1):c.2682C>T(p.Pro894=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00307 in 1,611,580 control chromosomes in the GnomAD database, including 254 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0070 ( 54 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 200 hom. )
Consequence
COL21A1
NM_030820.4 synonymous
NM_030820.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.122
Genes affected
COL21A1 (HGNC:17025): (collagen type XXI alpha 1 chain) This gene encodes the alpha chain of type XXI collagen, a member of the FACIT (fibril-associated collagens with interrupted helices) collagen family. Type XXI collagen is localized to tissues containing type I collagen and maintains the integrity of the extracellular matrix. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 6-56059169-G-A is Benign according to our data. Variant chr6-56059169-G-A is described in ClinVar as [Benign]. Clinvar id is 771399.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.122 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0628 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL21A1 | NM_030820.4 | c.2682C>T | p.Pro894= | synonymous_variant | 29/30 | ENST00000244728.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL21A1 | ENST00000244728.10 | c.2682C>T | p.Pro894= | synonymous_variant | 29/30 | 1 | NM_030820.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00704 AC: 1071AN: 152108Hom.: 54 Cov.: 32
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GnomAD3 exomes AF: 0.0119 AC: 2936AN: 246998Hom.: 170 AF XY: 0.00895 AC XY: 1200AN XY: 134054
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GnomAD4 exome AF: 0.00265 AC: 3868AN: 1459354Hom.: 200 Cov.: 30 AF XY: 0.00228 AC XY: 1656AN XY: 725972
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GnomAD4 genome AF: 0.00705 AC: 1073AN: 152226Hom.: 54 Cov.: 32 AF XY: 0.00820 AC XY: 610AN XY: 74420
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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 | Sep 17, 2017 | - - |
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