5-177992772-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006261.5(PROP1):c.618G>T(p.Leu206=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000202 in 1,581,728 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 (★). Synonymous variant affecting the same amino acid position (i.e. L206L) has been classified as Likely benign.
Frequency
Consequence
NM_006261.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROP1 | NM_006261.5 | c.618G>T | p.Leu206= | synonymous_variant | 3/3 | ENST00000308304.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROP1 | ENST00000308304.2 | c.618G>T | p.Leu206= | synonymous_variant | 3/3 | 1 | NM_006261.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000204 AC: 3AN: 147128Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000270 AC: 6AN: 222594Hom.: 0 AF XY: 0.0000168 AC XY: 2AN XY: 119370
GnomAD4 exome AF: 0.0000202 AC: 29AN: 1434600Hom.: 0 Cov.: 41 AF XY: 0.0000211 AC XY: 15AN XY: 710130
GnomAD4 genome AF: 0.0000204 AC: 3AN: 147128Hom.: 0 Cov.: 30 AF XY: 0.0000280 AC XY: 2AN XY: 71532
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at