NM_080680.3:c.5071-7C>T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_080680.3(COL11A2):c.5071-7C>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 0.00000496 in 1,612,908 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_080680.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL11A2 | NM_080680.3 | c.5071-7C>T | splice_region_variant, intron_variant | Intron 65 of 65 | ENST00000341947.7 | NP_542411.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL11A2 | ENST00000341947.7 | c.5071-7C>T | splice_region_variant, intron_variant | Intron 65 of 65 | 5 | NM_080680.3 | ENSP00000339915.2 | |||
COL11A2 | ENST00000374708.8 | c.4813-7C>T | splice_region_variant, intron_variant | Intron 63 of 63 | 5 | ENSP00000363840.4 | ||||
COL11A2 | ENST00000477772.1 | n.861-7C>T | splice_region_variant, intron_variant | Intron 8 of 8 | 2 | |||||
COL11A2 | ENST00000683572.1 | n.877-7C>T | splice_region_variant, intron_variant | Intron 8 of 8 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000164 AC: 4AN: 244202Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133370
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460638Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726642
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:2
COL11A2: BP4 -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at