rs117154313
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001849.4(COL6A2):c.116-34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 1,600,712 control chromosomes in the GnomAD database, including 615 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.020 ( 50 hom., cov: 32)
Exomes 𝑓: 0.024 ( 565 hom. )
Consequence
COL6A2
NM_001849.4 intron
NM_001849.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.39
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 Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 21-46111945-G-A is Benign according to our data. Variant chr21-46111945-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 93901.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-46111945-G-A is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0203 (3084/152262) while in subpopulation NFE AF= 0.0298 (2029/68006). AF 95% confidence interval is 0.0288. There are 50 homozygotes in gnomad4. There are 1504 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 50 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.116-34G>A | intron_variant | ENST00000300527.9 | |||
COL6A2 | NM_058174.3 | c.116-34G>A | intron_variant | ENST00000397763.6 | |||
LOC124905043 | XR_007067910.1 | n.87C>T | non_coding_transcript_exon_variant | 1/2 | |||
COL6A2 | NM_058175.3 | c.116-34G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.116-34G>A | intron_variant | 1 | NM_001849.4 | P1 | |||
COL6A2 | ENST00000397763.6 | c.116-34G>A | intron_variant | 5 | NM_058174.3 | ||||
COL6A2 | ENST00000409416.6 | c.116-34G>A | intron_variant | 5 | |||||
COL6A2 | ENST00000436769.5 | c.116-34G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0203 AC: 3083AN: 152144Hom.: 50 Cov.: 32
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GnomAD3 exomes AF: 0.0215 AC: 5232AN: 243146Hom.: 103 AF XY: 0.0218 AC XY: 2882AN XY: 132464
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GnomAD4 exome AF: 0.0242 AC: 35123AN: 1448450Hom.: 565 Cov.: 31 AF XY: 0.0239 AC XY: 17258AN XY: 721196
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GnomAD4 genome ? AF: 0.0203 AC: 3084AN: 152262Hom.: 50 Cov.: 32 AF XY: 0.0202 AC XY: 1504AN XY: 74448
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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
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 16, 2012 | - - |
Likely 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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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at