5-177994296-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_006261.5(PROP1):c.152G>T(p.Gly51Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000621 in 1,611,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G51A) has been classified as Benign.
Frequency
Consequence
NM_006261.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROP1 | NM_006261.5 | c.152G>T | p.Gly51Val | missense_variant | 2/3 | ENST00000308304.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROP1 | ENST00000308304.2 | c.152G>T | p.Gly51Val | missense_variant | 2/3 | 1 | NM_006261.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152114Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000222 AC: 54AN: 243052Hom.: 0 AF XY: 0.000227 AC XY: 30AN XY: 132006
GnomAD4 exome AF: 0.0000589 AC: 86AN: 1459246Hom.: 0 Cov.: 32 AF XY: 0.0000565 AC XY: 41AN XY: 725598
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152232Hom.: 0 Cov.: 31 AF XY: 0.0000806 AC XY: 6AN XY: 74434
ClinVar
Submissions by phenotype
Pituitary hormone deficiency, combined, 2 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 24, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at