1-78492766-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000959.4(PTGFR):c.23A>T(p.Gln8Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00499 in 1,613,658 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0041 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0051 ( 51 hom. )
Consequence
PTGFR
NM_000959.4 missense
NM_000959.4 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 3.04
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.003374815).
BP6
?
Variant 1-78492766-A-T is Benign according to our data. Variant chr1-78492766-A-T is described in ClinVar as [Benign]. Clinvar id is 720742.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00406 (619/152364) while in subpopulation SAS AF= 0.0205 (99/4832). AF 95% confidence interval is 0.0172. There are 2 homozygotes in gnomad4. There are 323 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGFR | NM_000959.4 | c.23A>T | p.Gln8Leu | missense_variant | 2/3 | ENST00000370757.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGFR | ENST00000370757.8 | c.23A>T | p.Gln8Leu | missense_variant | 2/3 | 1 | NM_000959.4 | P1 | |
PTGFR | ENST00000370758.5 | c.23A>T | p.Gln8Leu | missense_variant | 3/4 | 1 | P1 | ||
PTGFR | ENST00000370756.3 | c.23A>T | p.Gln8Leu | missense_variant | 2/4 | 1 | |||
PTGFR | ENST00000497923.5 | c.23A>T | p.Gln8Leu | missense_variant, NMD_transcript_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00408 AC: 621AN: 152246Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.00560 AC: 1404AN: 250892Hom.: 10 AF XY: 0.00659 AC XY: 894AN XY: 135598
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GnomAD4 exome AF: 0.00509 AC: 7438AN: 1461294Hom.: 51 Cov.: 30 AF XY: 0.00558 AC XY: 4058AN XY: 726948
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GnomAD4 genome ? AF: 0.00406 AC: 619AN: 152364Hom.: 2 Cov.: 33 AF XY: 0.00434 AC XY: 323AN XY: 74500
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27
ESP6500AA
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ESP6500EA
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49
ExAC
?
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707
Asia WGS
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58
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 07, 2018 | - - |
Computational scores
Source:
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
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
D;D;T
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MVP
MPC
0.21
ClinPred
T
GERP RS
Varity_R
gMVP
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