11-101127496-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000926.4(PGR):c.1575C>T(p.Tyr525=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,551,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
PGR
NM_000926.4 synonymous
NM_000926.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.20
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 11-101127496-G-A is Benign according to our data. Variant chr11-101127496-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 738291.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.2 with no splicing effect.
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGR | NM_000926.4 | c.1575C>T | p.Tyr525= | synonymous_variant | 1/8 | ENST00000325455.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGR | ENST00000325455.10 | c.1575C>T | p.Tyr525= | synonymous_variant | 1/8 | 1 | NM_000926.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152050Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000154 AC: 23AN: 149484Hom.: 0 AF XY: 0.000167 AC XY: 14AN XY: 83884
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GnomAD4 exome AF: 0.000103 AC: 144AN: 1399316Hom.: 0 Cov.: 31 AF XY: 0.000110 AC XY: 76AN XY: 693350
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GnomAD4 genome AF: 0.0000921 AC: 14AN: 152050Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74268
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at