rs5275
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000963.4(PTGS2):c.*427T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151922 control chromosomes in the gnomAD Genomes database, including 13726 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other (no stars).
Frequency
Genomes: đť‘“ 0.40 ( 13726 hom., cov: 33)
Consequence
PTGS2
NM_000963.4 3_prime_UTR
NM_000963.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.15
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGS2 | NM_000963.4 | c.*427T>C | 3_prime_UTR_variant | 10/10 | ENST00000367468.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGS2 | ENST00000367468.10 | c.*427T>C | 3_prime_UTR_variant | 10/10 | 1 | NM_000963.4 | P1 | ||
PTGS2 | ENST00000490885.6 | n.2657T>C | non_coding_transcript_exon_variant | 9/9 | 1 | ||||
PTGS2 | ENST00000680451.1 | c.*427T>C | 3_prime_UTR_variant | 11/11 | P1 | ||||
PTGS2 | ENST00000681605.1 | c.*1914T>C | 3_prime_UTR_variant, NMD_transcript_variant | 10/10 |
Frequencies
GnomAD3 genomes AF: 0.404 AC: 61413AN: 151922Hom.: 13726 Cov.: 33
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GnomAD4 exome AF: 0.347 AC: 127AN: 366Hom.: 18 AF XY: 0.357 AC XY: 80AN XY: 224
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ClinVar
Significance: other
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Cholangiocarcinoma Other:1
other, no assertion criteria provided | research | Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin | Dec 10, 2022 | No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at