chr21-45986693-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001848.3(COL6A1):c.588+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000123 in 1,542,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001848.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.588+8C>T | splice_region_variant, intron_variant | Intron 4 of 34 | ENST00000361866.8 | NP_001839.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000674 AC: 1AN: 148460Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000129 AC: 18AN: 1393732Hom.: 0 Cov.: 33 AF XY: 0.0000131 AC XY: 9AN XY: 687544
GnomAD4 genome AF: 0.00000674 AC: 1AN: 148460Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 1AN XY: 72472
ClinVar
Submissions by phenotype
Bethlem myopathy 1A Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at