rs200141347
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001261430.2(PTGES3L):c.433-8_433-7del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 727,068 control chromosomes in the GnomAD database, including 192 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 78 hom., cov: 0)
Exomes 𝑓: 0.032 ( 114 hom. )
Consequence
PTGES3L
NM_001261430.2 splice_region, splice_polypyrimidine_tract, intron
NM_001261430.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.192
Genes affected
PTGES3L (HGNC:43943): (prostaglandin E synthase 3 like) Predicted to enable Hsp90 protein binding activity and chaperone binding activity. Predicted to be involved in chaperone-mediated protein complex assembly and protein folding. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 17-42969192-GGC-G is Benign according to our data. Variant chr17-42969192-GGC-G is described in ClinVar as [Benign]. Clinvar id is 403353.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGES3L | NM_001261430.2 | c.433-8_433-7del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000591916.7 | |||
PTGES3L-AARSD1 | NM_001136042.2 | c.561+1095_561+1096del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGES3L | ENST00000591916.7 | c.433-8_433-7del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 3 | NM_001261430.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.158 AC: 2606AN: 16442Hom.: 78 Cov.: 0
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GnomAD4 exome AF: 0.0319 AC: 22641AN: 710560Hom.: 114 AF XY: 0.0330 AC XY: 11425AN XY: 346558
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GnomAD4 genome AF: 0.159 AC: 2618AN: 16508Hom.: 78 Cov.: 0 AF XY: 0.159 AC XY: 1299AN XY: 8156
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at