NM_004369.4:c.92-59T>C
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004369.4(COL6A3):c.92-59T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,582,598 control chromosomes in the GnomAD database, including 66,551 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004369.4 intron
Scores
Clinical Significance
Conservation
Publications
- Bethlem myopathy 1AInheritance: AD, AR, SD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Ambry Genetics
- collagen 6-related myopathyInheritance: AD, AR Classification: DEFINITIVE Submitted by: ClinGen
- Ullrich congenital muscular dystrophy 1CInheritance: AR Classification: DEFINITIVE Submitted by: G2P
- dystonia 27Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED, NO_KNOWN Submitted by: Illumina, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Orphanet
- Ullrich congenital muscular dystrophy 1AInheritance: AR, AD, SD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp
- Bethlem myopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Ullrich congenital muscular dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.357 AC: 54198AN: 152022Hom.: 11163 Cov.: 33 show subpopulations
GnomAD4 exome AF: 0.271 AC: 388321AN: 1430458Hom.: 55352 AF XY: 0.270 AC XY: 192203AN XY: 711620 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.357 AC: 54294AN: 152140Hom.: 11199 Cov.: 33 AF XY: 0.359 AC XY: 26721AN XY: 74390 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 56% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 52. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at