rs199513044
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001849.4(COL6A2):c.1333-10C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000263 in 1,521,328 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001849.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.1333-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000300527.9 | |||
COL6A2 | NM_058174.3 | c.1333-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000397763.6 | |||
COL6A2 | NM_058175.3 | c.1333-10C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.1333-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001849.4 | P1 | |||
COL6A2 | ENST00000397763.6 | c.1333-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_058174.3 | ||||
COL6A2 | ENST00000409416.6 | c.1333-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.00000219 AC: 3AN: 1369134Hom.: 0 Cov.: 30 AF XY: 0.00000296 AC XY: 2AN XY: 674988
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at