13-113158648-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003891.3(PROZ):c.-13G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 1,596,626 control chromosomes in the GnomAD database, including 626,754 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.81 ( 51325 hom., cov: 31)
Exomes 𝑓: 0.89 ( 575429 hom. )
Consequence
PROZ
NM_003891.3 5_prime_UTR
NM_003891.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.838
Genes affected
PROZ (HGNC:9460): (protein Z, vitamin K dependent plasma glycoprotein) This gene encodes a liver vitamin K-dependent glycoprotein that is synthesized in the liver and secreted into the plasma. The encoded protein plays a role in regulating blood coagulation by complexing with protein Z-dependent protease inhibitor to directly inhibit activated factor X at the phospholipid surface. Deficiencies in this protein are associated with an increased risk of ischemic arterial diseases and fetal loss. Mutations in this gene are the cause of protein Z deficiency. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROZ | NM_003891.3 | c.-13G>A | 5_prime_UTR_variant | 1/8 | ENST00000375547.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROZ | ENST00000375547.7 | c.-13G>A | 5_prime_UTR_variant | 1/8 | 1 | NM_003891.3 | P2 | ||
PROZ | ENST00000342783.5 | c.-13G>A | 5_prime_UTR_variant | 1/9 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.810 AC: 123042AN: 151862Hom.: 51322 Cov.: 31
GnomAD3 genomes
AF:
AC:
123042
AN:
151862
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.797 AC: 179295AN: 224854Hom.: 74515 AF XY: 0.803 AC XY: 97752AN XY: 121728
GnomAD3 exomes
AF:
AC:
179295
AN:
224854
Hom.:
AF XY:
AC XY:
97752
AN XY:
121728
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.885 AC: 1278779AN: 1444646Hom.: 575429 Cov.: 42 AF XY: 0.880 AC XY: 631453AN XY: 717578
GnomAD4 exome
AF:
AC:
1278779
AN:
1444646
Hom.:
Cov.:
42
AF XY:
AC XY:
631453
AN XY:
717578
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.810 AC: 123081AN: 151980Hom.: 51325 Cov.: 31 AF XY: 0.800 AC XY: 59408AN XY: 74266
GnomAD4 genome
AF:
AC:
123081
AN:
151980
Hom.:
Cov.:
31
AF XY:
AC XY:
59408
AN XY:
74266
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1809
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at