rs3128925
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000441798.1(COL11A2P1):n.647G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 683,990 control chromosomes in the GnomAD database, including 19,146 homozygotes. 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
Genomes: 𝑓 0.27 ( 6210 hom., cov: 30)
Exomes 𝑓: 0.21 ( 12936 hom. )
Consequence
COL11A2P1
ENST00000441798.1 non_coding_transcript_exon
ENST00000441798.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.47
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL11A2P1 | ENST00000441798.1 | n.647G>T | non_coding_transcript_exon_variant | 6/6 |
Frequencies
GnomAD3 genomes ? AF: 0.272 AC: 41341AN: 151750Hom.: 6203 Cov.: 30
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GnomAD4 exome AF: 0.209 AC: 111351AN: 532120Hom.: 12936 Cov.: 4 AF XY: 0.210 AC XY: 61506AN XY: 292310
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GnomAD4 genome ? AF: 0.272 AC: 41366AN: 151870Hom.: 6210 Cov.: 30 AF XY: 0.268 AC XY: 19900AN XY: 74246
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at