rs908989305
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001849.4(COL6A2):c.1845C>T(p.Asp615=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
COL6A2
NM_001849.4 synonymous
NM_001849.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.352
Genes affected
COL6A2 (HGNC:2212): (collagen type VI alpha 2 chain) This gene encodes one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The product of this gene contains several domains similar to von Willebrand Factor type A domains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in this gene are associated with Bethlem myopathy and Ullrich scleroatonic muscular dystrophy. Three transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
?
Variant 21-46125493-C-T is Benign according to our data. Variant chr21-46125493-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 543005.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.352 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.1845C>T | p.Asp615= | synonymous_variant | 25/28 | ENST00000300527.9 | |
COL6A2 | NM_058174.3 | c.1845C>T | p.Asp615= | synonymous_variant | 25/28 | ENST00000397763.6 | |
COL6A2 | NM_058175.3 | c.1845C>T | p.Asp615= | synonymous_variant | 25/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.1845C>T | p.Asp615= | synonymous_variant | 25/28 | 1 | NM_001849.4 | P1 | |
COL6A2 | ENST00000397763.6 | c.1845C>T | p.Asp615= | synonymous_variant | 25/28 | 5 | NM_058174.3 | ||
COL6A2 | ENST00000409416.6 | c.1845C>T | p.Asp615= | synonymous_variant | 24/27 | 5 | |||
COL6A2 | ENST00000413758.1 | c.516C>T | p.Asp172= | synonymous_variant | 10/11 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250648Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135818
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460664Hom.: 0 Cov.: 52 AF XY: 0.00000138 AC XY: 1AN XY: 726634
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GnomAD4 genome ? Cov.: 33
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
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