20-35201339-C-A

Variant names:

• chr20-35201339-C-A
• rs8114671
• NM_001355008.2:c.-102+16473G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001355008.2(MMP24-AS1-EDEM2):​c.-102+16473G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,998 control chromosomes in the GnomAD database, including 13,303 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 0.41 (13303 hom., cov: 32)
• Consequence: MMP24-AS1-EDEM2 NM_001355008.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 23 publications found

Genes affected

MMP24-AS1-EDEM2 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMP24-AS1-EDEM2	NM_001355008.2	c.-102+16473G>T		intron_variant	Intron 4 of 14		NP_001341937.1
PROCR	XM_011528496.2	c.713-14554C>A		intron_variant	Intron 4 of 4		XP_011526798.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PROCR	ENST00000635377.1	c.629-14554C>A		intron_variant	Intron 3 of 3	5		ENSP00000489117.1
PROCR	ENST00000634509.1	c.95-14554C>A		intron_variant	Intron 1 of 1	3		ENSP00000489456.1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61767 AN: 151882 Hom.: 13299 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.432

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.406 AC: 61773 AN: 151998 Hom.: 13303 Cov.: 32 AF XY: 0.406 AC XY: 30147 AN XY: 74278

African (AFR) AF: 0.274 AC: 11350 AN: 41462

American (AMR) AF: 0.522 AC: 7958 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1396 AN: 3472

East Asian (EAS) AF: 0.640 AC: 3312 AN: 5178

South Asian (SAS) AF: 0.327 AC: 1575 AN: 4822

European-Finnish (FIN) AF: 0.431 AC: 4539 AN: 10528

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30150 AN: 67974

Other (OTH) AF: 0.427 AC: 902 AN: 2110

Alfa AF: 0.419 Hom.: 19647

Bravo AF: 0.417

Asia WGS AF: 0.415 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.37
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs8114671; hg19: chr20-33789142;