1-78493396-T-C
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000959.4(PTGFR):āc.653T>Cā(p.Leu218Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000771 in 1,613,852 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0042 ( 7 hom., cov: 33)
Exomes š: 0.00042 ( 2 hom. )
Consequence
PTGFR
NM_000959.4 missense
NM_000959.4 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 3.94
Genes affected
PTGFR (HGNC:9600): (prostaglandin F receptor) The protein encoded by this gene is member of the G-protein coupled receptor family. This protein is a receptor for prostaglandin F2-alpha (PGF2-alpha), which is known to be a potent luteolytic agent, and may also be involved in modulating intraocular pressure and smooth muscle contraction in uterus. Knockout studies in mice suggest that the interaction of PGF2-alpha with this receptor may initiate parturition in ovarian luteal cells and thus induce luteolysis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0074677765).
BP6
Variant 1-78493396-T-C is Benign according to our data. Variant chr1-78493396-T-C is described in ClinVar as [Benign]. Clinvar id is 711770.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTGFR | NM_000959.4 | c.653T>C | p.Leu218Ser | missense_variant | 2/3 | ENST00000370757.8 | NP_000950.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGFR | ENST00000370757.8 | c.653T>C | p.Leu218Ser | missense_variant | 2/3 | 1 | NM_000959.4 | ENSP00000359793 | P1 | |
PTGFR | ENST00000370758.5 | c.653T>C | p.Leu218Ser | missense_variant | 3/4 | 1 | ENSP00000359794 | P1 | ||
PTGFR | ENST00000370756.3 | c.653T>C | p.Leu218Ser | missense_variant | 2/4 | 1 | ENSP00000359792 | |||
PTGFR | ENST00000497923.5 | c.653T>C | p.Leu218Ser | missense_variant, NMD_transcript_variant | 2/5 | 3 | ENSP00000432599 |
Frequencies
GnomAD3 genomes AF: 0.00416 AC: 634AN: 152236Hom.: 7 Cov.: 33
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GnomAD3 exomes AF: 0.00109 AC: 273AN: 250118Hom.: 2 AF XY: 0.000717 AC XY: 97AN XY: 135294
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GnomAD4 exome AF: 0.000418 AC: 611AN: 1461498Hom.: 2 Cov.: 31 AF XY: 0.000347 AC XY: 252AN XY: 727016
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GnomAD4 genome AF: 0.00415 AC: 633AN: 152354Hom.: 7 Cov.: 33 AF XY: 0.00393 AC XY: 293AN XY: 74514
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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
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MVP
MPC
0.31
ClinPred
T
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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