rs3740753
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000926.4(PGR):āc.1031G>Cā(p.Ser344Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,605,944 control chromosomes in the GnomAD database, including 19,352 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000926.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGR | NM_000926.4 | c.1031G>C | p.Ser344Thr | missense_variant | 1/8 | ENST00000325455.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGR | ENST00000325455.10 | c.1031G>C | p.Ser344Thr | missense_variant | 1/8 | 1 | NM_000926.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.117 AC: 17840AN: 152008Hom.: 1367 Cov.: 33
GnomAD3 exomes AF: 0.132 AC: 30549AN: 231704Hom.: 2403 AF XY: 0.132 AC XY: 16917AN XY: 128452
GnomAD4 exome AF: 0.152 AC: 220890AN: 1453818Hom.: 17986 Cov.: 41 AF XY: 0.150 AC XY: 108320AN XY: 723640
GnomAD4 genome ? AF: 0.117 AC: 17839AN: 152126Hom.: 1366 Cov.: 33 AF XY: 0.115 AC XY: 8578AN XY: 74388
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at