rs669661

Positions:

• chr11-57380702-A-G
• chr11-57380702-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006093.4(PRG3):​c.7T>C​(p.Cys3Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.993 in 1,555,408 control chromosomes in the GnomAD database, including 766,868 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.96 (70708 hom., cov: 32)
  • Exomes 𝑓: 1.0 (696160 hom.)
• Consequence: PRG3 NM_006093.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884

Genes affected

PRG3 (HGNC:9363): (proteoglycan 3, pro eosinophil major basic protein 2) An extracellular matrix structural constituent conferring compression resistance. Involved in several processes, including granulocyte activation; histamine biosynthetic process; and regulation of gene expression. Located in collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.5357821E-6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRG3	NM_006093.4	c.7T>C	p.Cys3Arg	missense_variant	2/6	ENST00000287143.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRG3	ENST00000287143.2	c.7T>C	p.Cys3Arg	missense_variant	2/6	1	NM_006093.4	P1

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146326 AN: 152154 Hom.: 70671 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.994

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.971

GnomAD3 exomes AF: 0.989 AC: 189461 AN: 191506 Hom.: 93829 AF XY: 0.992 AC XY: 104137 AN XY: 104936

Gnomad AFR exome AF: 0.859

Gnomad AMR exome AF: 0.993

Gnomad ASJ exome AF: 1.00

Gnomad EAS exome AF: 0.999

Gnomad SAS exome AF: 0.995

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 1.00

Gnomad OTH exome AF: 0.995

GnomAD4 exome AF: 0.996 AC: 1397371 AN: 1403136 Hom.: 696160 Cov.: 41 AF XY: 0.996 AC XY: 693886 AN XY: 696440

Gnomad4 AFR exome AF: 0.856

Gnomad4 AMR exome AF: 0.992

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.996

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.991

GnomAD4 genome AF: 0.962 AC: 146420 AN: 152272 Hom.: 70708 Cov.: 32 AF XY: 0.964 AC XY: 71739 AN XY: 74454

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.987

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.999

Gnomad4 OTH AF: 0.971

Alfa AF: 0.994 Hom.: 110252

Bravo AF: 0.956

TwinsUK AF: 1.00 AC: 3707

ALSPAC AF: 1.00 AC: 3854

ESP6500AA AF: 0.867 AC: 3815

ESP6500EA AF: 0.999 AC: 8583

ExAC AF: 0.986 AC: 119344

Asia WGS AF: 0.984 AC: 3423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.082
BayesDel_addAF	Benign	-0.84	T
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.54
DEOGEN2	Benign	0.0079	T
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.0039	N
LIST_S2	Benign	0.15	T
MetaRNN	Benign	0.0000015	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.69	N
MutationTaster	Benign	1.0	P
PrimateAI	Benign	0.21	T
PROVEAN	Benign	0.62	N
REVEL	Benign	0.014
Sift	Benign	0.88	T
Sift4G	Benign	0.70	T
Polyphen		0.0	B
Vest4		0.036
MPC		0.24
ClinPred		0.00087	T
GERP RS		-6.0
Varity_R		0.10
gMVP		0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs669661; hg19: chr11-57148175;