2-237339123-G-GA
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_004369.4(COL6A3):c.8465-7_8465-6insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,596,736 control chromosomes in the GnomAD database, including 1 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004369.4 splice_region, splice_polypyrimidine_tract, 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.8465-7_8465-6insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000295550.9 | |||
COL6A3 | NM_057166.5 | c.6644-7_6644-6insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
COL6A3 | NM_057167.4 | c.7847-7_7847-6insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.8465-7_8465-6insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004369.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 151452Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000408 AC: 101AN: 247528Hom.: 1 AF XY: 0.000254 AC XY: 34AN XY: 133964
GnomAD4 exome AF: 0.000176 AC: 255AN: 1445168Hom.: 1 Cov.: 26 AF XY: 0.000140 AC XY: 101AN XY: 719780
GnomAD4 genome AF: 0.000112 AC: 17AN: 151568Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74062
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 15, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Bethlem myopathy 1A Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 12, 2023 | See Variant Classification Assertion Criteria. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at