rs484389
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000926.4(PGR):c.*38T>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 0.243 in 1,551,512 control chromosomes in the GnomAD database, including 47,866 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.28 ( 6474 hom., cov: 32)
Exomes 𝑓: 0.24 ( 41392 hom. )
Consequence
PGR
NM_000926.4 3_prime_UTR
NM_000926.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.36
Genes affected
PGR (HGNC:8910): (progesterone receptor) This gene encodes a member of the steroid receptor superfamily. The encoded protein mediates the physiological effects of progesterone, which plays a central role in reproductive events associated with the establishment and maintenance of pregnancy. This gene uses two distinct promotors and translation start sites in the first exon to produce several transcript variants, both protein coding and non-protein coding. Two of the isoforms (A and B) are identical except for an additional 165 amino acids found in the N-terminus of isoform B and mediate their own response genes and physiologic effects with little overlap. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGR | NM_000926.4 | c.*38T>C | 3_prime_UTR_variant | 8/8 | ENST00000325455.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGR | ENST00000325455.10 | c.*38T>C | 3_prime_UTR_variant | 8/8 | 1 | NM_000926.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.284 AC: 42987AN: 151562Hom.: 6455 Cov.: 32
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GnomAD3 exomes AF: 0.241 AC: 59220AN: 246110Hom.: 7681 AF XY: 0.232 AC XY: 31020AN XY: 133672
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GnomAD4 exome AF: 0.238 AC: 333808AN: 1399832Hom.: 41392 Cov.: 23 AF XY: 0.234 AC XY: 163977AN XY: 699824
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GnomAD4 genome ? AF: 0.284 AC: 43068AN: 151680Hom.: 6474 Cov.: 32 AF XY: 0.278 AC XY: 20616AN XY: 74166
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ClinVar
Not reported inComputational scores
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Name
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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