6-70300186-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001851.6(COL9A1):c.167-11C>A 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 0.00000248 in 1,613,244 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_001851.6 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL9A1 | NM_001851.6 | c.167-11C>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000357250.11 | |||
COL9A1 | NM_001377291.1 | c.167-11C>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
COL9A1 | XM_011535429.4 | c.167-11C>A | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL9A1 | ENST00000357250.11 | c.167-11C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001851.6 | P1 | |||
COL9A1 | ENST00000370496.3 | c.167-11C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151766Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250816Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135604
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461478Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727056
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151766Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74128
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at