6-30562719-T-C

Variant names:

• chr6-30562719-T-C
• rs2074503
• NM_025263.4:c.*224T>C

Variant summary

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

The NM_025263.4(PRR3):​c.*224T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 417,860 control chromosomes in the GnomAD database, including 105,665 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 0.73 (40932 hom., cov: 33)
  • Exomes 𝑓: 0.69 (64733 hom.)
• Consequence: PRR3 NM_025263.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 27 publications found

Genes affected

PRR3 (HGNC:21149): (proline rich 3) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000290047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025263.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR3	NM_025263.4	MANE Select	c.*224T>C		3_prime_UTR	Exon 4 of 4	NP_079539.2	P79522-1
	PRR3	NM_001077497.3		c.*224T>C		3_prime_UTR	Exon 3 of 3	NP_001070965.1	P79522-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR3	ENST00000376560.8	TSL:1 MANE Select	c.*224T>C		3_prime_UTR	Exon 4 of 4	ENSP00000365744.4	P79522-1
	PRR3	ENST00000376557.3	TSL:2	c.*224T>C		3_prime_UTR	Exon 3 of 3	ENSP00000365740.3	P79522-2
	PRR3	ENST00000934408.1		c.*224T>C		3_prime_UTR	Exon 2 of 2	ENSP00000604467.1

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110949 AN: 152088 Hom.: 40885 Cov.: 33

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.727

GnomAD4 exome AF: 0.694 AC: 184375 AN: 265652 Hom.: 64733 Cov.: 2 AF XY: 0.696 AC XY: 95052 AN XY: 136580

African (AFR) AF: 0.841 AC: 6274 AN: 7456

American (AMR) AF: 0.653 AC: 5919 AN: 9062

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 7582 AN: 9198

East Asian (EAS) AF: 0.723 AC: 16502 AN: 22840

South Asian (SAS) AF: 0.779 AC: 8257 AN: 10606

European-Finnish (FIN) AF: 0.672 AC: 14207 AN: 21156

Middle Eastern (MID) AF: 0.798 AC: 1049 AN: 1314

European-Non Finnish (NFE) AF: 0.673 AC: 112445 AN: 167116

Other (OTH) AF: 0.718 AC: 12140 AN: 16904

GnomAD4 genome AF: 0.730 AC: 111055 AN: 152208 Hom.: 40932 Cov.: 33 AF XY: 0.727 AC XY: 54068 AN XY: 74408

African (AFR) AF: 0.840 AC: 34881 AN: 41534

American (AMR) AF: 0.652 AC: 9960 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2890 AN: 3472

East Asian (EAS) AF: 0.697 AC: 3608 AN: 5180

South Asian (SAS) AF: 0.829 AC: 4000 AN: 4826

European-Finnish (FIN) AF: 0.680 AC: 7209 AN: 10594

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46048 AN: 68004

Other (OTH) AF: 0.730 AC: 1543 AN: 2114

Alfa AF: 0.699 Hom.: 134276

Bravo AF: 0.732

Asia WGS AF: 0.784 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.17
PhyloP100		-2.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2074503; hg19: chr6-30530496;