rs1042838
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000926.4(PGR):c.1978G>T(p.Val660Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,613,600 control chromosomes in the GnomAD database, including 19,162 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PGR | NM_000926.4 | c.1978G>T | p.Val660Leu | missense_variant | 4/8 | ENST00000325455.10 | NP_000917.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGR | ENST00000325455.10 | c.1978G>T | p.Val660Leu | missense_variant | 4/8 | 1 | NM_000926.4 | ENSP00000325120 | P1 |
Frequencies
GnomAD3 genomes AF: 0.116 AC: 17607AN: 152036Hom.: 1325 Cov.: 32
GnomAD3 exomes AF: 0.130 AC: 32533AN: 250006Hom.: 2561 AF XY: 0.130 AC XY: 17615AN XY: 135084
GnomAD4 exome AF: 0.151 AC: 220053AN: 1461446Hom.: 17838 Cov.: 33 AF XY: 0.148 AC XY: 107783AN XY: 727032
GnomAD4 genome AF: 0.116 AC: 17607AN: 152154Hom.: 1324 Cov.: 32 AF XY: 0.114 AC XY: 8469AN XY: 74368
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at