6-33163559-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_080680.3(COL11A2):c.*119G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000876 in 1,525,812 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_080680.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL11A2 | NM_080680.3 | c.*119G>A | 3_prime_UTR_variant | Exon 66 of 66 | ENST00000341947.7 | NP_542411.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL11A2 | ENST00000341947 | c.*119G>A | 3_prime_UTR_variant | Exon 66 of 66 | 5 | NM_080680.3 | ENSP00000339915.2 | |||
COL11A2 | ENST00000374708 | c.*119G>A | 3_prime_UTR_variant | Exon 64 of 64 | 5 | ENSP00000363840.4 | ||||
COL11A2 | ENST00000477772.1 | n.1120G>A | non_coding_transcript_exon_variant | Exon 9 of 9 | 2 | |||||
COL11A2 | ENST00000683572.1 | n.1136G>A | non_coding_transcript_exon_variant | Exon 9 of 9 |
Frequencies
GnomAD3 genomes AF: 0.00338 AC: 514AN: 152086Hom.: 2 Cov.: 32
GnomAD4 exome AF: 0.000597 AC: 820AN: 1373608Hom.: 4 Cov.: 24 AF XY: 0.000542 AC XY: 371AN XY: 684520
GnomAD4 genome AF: 0.00339 AC: 516AN: 152204Hom.: 2 Cov.: 32 AF XY: 0.00337 AC XY: 251AN XY: 74420
ClinVar
Submissions by phenotype
Otospondylomegaepiphyseal dysplasia, autosomal dominant Benign:1
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Otospondylomegaepiphyseal dysplasia, autosomal recessive Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Fibrochondrogenesis 2 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Stickler Syndrome, Dominant Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at