rs9574

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_006404.5(PROCR):​c.*16C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000561 in 1,611,156 control chromosomes in the GnomAD database, including 8 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 0.00043 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00057 ( 8 hom. )

Consequence

PROCR
NM_006404.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.369
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS2
High Homozygotes in GnomAdExome4 at 8 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PROCRNM_006404.5 linkuse as main transcriptc.*16C>A 3_prime_UTR_variant 4/4 ENST00000216968.5
MMP24-AS1-EDEM2NM_001355008.2 linkuse as main transcriptc.-101-10958G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PROCRENST00000216968.5 linkuse as main transcriptc.*16C>A 3_prime_UTR_variant 4/41 NM_006404.5 P1
PROCRENST00000634509.1 linkuse as main transcriptc.94+383C>A intron_variant 3
PROCRENST00000635377.1 linkuse as main transcriptc.502-258C>A intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.000435
AC:
66
AN:
151848
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000852
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00290
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000412
Gnomad OTH
AF:
0.000960
GnomAD3 exomes
AF:
0.00111
AC:
273
AN:
246476
Hom.:
0
AF XY:
0.00126
AC XY:
168
AN XY:
133258
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00151
Gnomad ASJ exome
AF:
0.00311
Gnomad EAS exome
AF:
0.0000554
Gnomad SAS exome
AF:
0.00420
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000467
Gnomad OTH exome
AF:
0.00199
GnomAD4 exome
AF:
0.000574
AC:
838
AN:
1459188
Hom.:
8
Cov.:
60
AF XY:
0.000670
AC XY:
486
AN XY:
725580
show subpopulations
Gnomad4 AFR exome
AF:
0.000478
Gnomad4 AMR exome
AF:
0.00138
Gnomad4 ASJ exome
AF:
0.00211
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00387
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000222
Gnomad4 OTH exome
AF:
0.000978
GnomAD4 genome
AF:
0.000434
AC:
66
AN:
151968
Hom.:
0
Cov.:
30
AF XY:
0.000472
AC XY:
35
AN XY:
74228
show subpopulations
Gnomad4 AFR
AF:
0.000121
Gnomad4 AMR
AF:
0.000851
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00291
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000412
Gnomad4 OTH
AF:
0.000950
Alfa
AF:
0.00122
Hom.:
2631

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
8.6
DANN
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9574; hg19: chr20-33764632; API