NM_000962.4:c.123G>A
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000962.4(PTGS1):c.123G>A(p.Gln41Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0377 in 1,613,848 control chromosomes in the GnomAD database, including 3,199 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.092 ( 1356 hom., cov: 33)
Exomes 𝑓: 0.032 ( 1843 hom. )
Consequence
PTGS1
NM_000962.4 synonymous
NM_000962.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.48
Genes affected
PTGS1 (HGNC:9604): (prostaglandin-endoperoxide synthase 1) This is one of two genes encoding similar enzymes that catalyze the conversion of arachidonate to prostaglandin. The encoded protein regulates angiogenesis in endothelial cells, and is inhibited by nonsteroidal anti-inflammatory drugs such as aspirin. Based on its ability to function as both a cyclooxygenase and as a peroxidase, the encoded protein has been identified as a moonlighting protein. The protein may promote cell proliferation during tumor progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2021]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 9-122377927-G-A is Benign according to our data. Variant chr9-122377927-G-A is described in ClinVar as [Benign]. Clinvar id is 1241842.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=3.48 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0917 AC: 13950AN: 152126Hom.: 1357 Cov.: 33
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GnomAD3 exomes AF: 0.0462 AC: 11613AN: 251310Hom.: 678 AF XY: 0.0427 AC XY: 5807AN XY: 135852
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GnomAD4 exome AF: 0.0320 AC: 46799AN: 1461604Hom.: 1843 Cov.: 31 AF XY: 0.0319 AC XY: 23211AN XY: 727138
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GnomAD4 genome AF: 0.0918 AC: 13970AN: 152244Hom.: 1356 Cov.: 33 AF XY: 0.0895 AC XY: 6665AN XY: 74448
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
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Dec 08, 2020
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at