chr7-101128467-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000602.5(SERPINE1):c.74A>C(p.His25Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000545 in 1,614,120 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000602.5 missense
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 |
---|---|---|---|---|---|---|---|
SERPINE1 | NM_000602.5 | c.74A>C | p.His25Pro | missense_variant | 2/9 | ENST00000223095.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINE1 | ENST00000223095.5 | c.74A>C | p.His25Pro | missense_variant | 2/9 | 1 | NM_000602.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251308Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135832
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461884Hom.: 0 Cov.: 33 AF XY: 0.0000289 AC XY: 21AN XY: 727242
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000390 AC XY: 29AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at