rs663550
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001355008.2(MMP24-AS1-EDEM2):c.-101-25594T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00265 in 151,586 control chromosomes in the GnomAD database, including 2 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 0.0026 ( 2 hom., cov: 31)
Consequence
MMP24-AS1-EDEM2
NM_001355008.2 intron
NM_001355008.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.224
Genes affected
PROCR (HGNC:9452): (protein C receptor) The protein encoded by this gene is a receptor for activated protein C, a serine protease activated by and involved in the blood coagulation pathway. The encoded protein is an N-glycosylated type I membrane protein that enhances the activation of protein C. Mutations in this gene have been associated with venous thromboembolism and myocardial infarction, as well as with late fetal loss during pregnancy. The encoded protein may also play a role in malarial infection and has been associated with cancer. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BS2
High Homozygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP24-AS1-EDEM2 | NM_001355008.2 | c.-101-25594T>G | intron_variant | ||||
PROCR | XM_011528496.2 | c.712+15019A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROCR | ENST00000634509.1 | c.94+15019A>C | intron_variant | 3 | |||||
PROCR | ENST00000635377.1 | c.630+14250A>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00266 AC: 403AN: 151468Hom.: 2 Cov.: 31
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GnomAD4 genome AF: 0.00265 AC: 401AN: 151586Hom.: 2 Cov.: 31 AF XY: 0.00265 AC XY: 196AN XY: 74034
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at