rs553575841
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The ENST00000322507.13(COL12A1):āc.6345A>Gā(p.Gly2115=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000209 in 1,608,728 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00011 ( 0 hom., cov: 32)
Exomes š: 0.00022 ( 3 hom. )
Consequence
COL12A1
ENST00000322507.13 synonymous
ENST00000322507.13 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.283
Genes affected
COL12A1 (HGNC:2188): (collagen type XII alpha 1 chain) This gene encodes the alpha chain of type XII collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XII collagen is a homotrimer found in association with type I collagen, an association that is thought to modify the interactions between collagen I fibrils and the surrounding matrix. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 6-75126466-T-C is Benign according to our data. Variant chr6-75126466-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 475886.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.283 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000105 (16/151938) while in subpopulation SAS AF= 0.00208 (10/4804). AF 95% confidence interval is 0.00113. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 3 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.6345A>G | p.Gly2115= | synonymous_variant | 39/66 | ENST00000322507.13 | NP_004361.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.6345A>G | p.Gly2115= | synonymous_variant | 39/66 | 1 | NM_004370.6 | ENSP00000325146 | P4 | |
COL12A1 | ENST00000345356.10 | c.2853A>G | p.Gly951= | synonymous_variant | 24/51 | 1 | ENSP00000305147 | |||
COL12A1 | ENST00000483888.6 | c.6345A>G | p.Gly2115= | synonymous_variant | 39/65 | 5 | ENSP00000421216 | A1 | ||
COL12A1 | ENST00000416123.6 | c.6345A>G | p.Gly2115= | synonymous_variant | 38/63 | 5 | ENSP00000412864 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 151820Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000456 AC: 113AN: 247948Hom.: 1 AF XY: 0.000699 AC XY: 94AN XY: 134506
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GnomAD4 exome AF: 0.000220 AC: 321AN: 1456790Hom.: 3 Cov.: 30 AF XY: 0.000349 AC XY: 253AN XY: 724684
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GnomAD4 genome AF: 0.000105 AC: 16AN: 151938Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74272
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 30, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 01, 2021 | - - |
Computational scores
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Name
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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