rs2304679

chr2-27138354-G-A

Variant summary

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

The NM_178553.4(PRR30):c.-25C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00356 in 1,569,448 control chromosomes in the GnomAD database, including 207 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 0.0043 (15 hom., cov: 32)
  • Exomes 𝑓: 0.0035 (192 hom.)
• Consequence: PRR30 NM_178553.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

Genes affected

PRR30 (HGNC:28677): (proline rich 30)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRR30	NM_178553.4	c.-25C>T		5_prime_UTR_variant	3/3	ENST00000335524.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRR30	ENST00000335524.7	c.-25C>T		5_prime_UTR_variant	3/3	1	NM_178553.4	P1
PRR30	ENST00000432962.2	c.-25C>T		5_prime_UTR_variant	3/4	3

Frequencies

GnomAD3 genomes AF: 0.00429 AC: 653 AN: 152182 Hom.: 15 Cov.: 32

Gnomad AFR AF: 0.000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00995

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.00301

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000456

Gnomad OTH AF: 0.00669

GnomAD3 exomes AF: 0.00863 AC: 1846 AN: 213908 Hom.: 50 AF XY: 0.00753 AC XY: 863 AN XY: 114568

Gnomad AFR exome AF: 0.000699

Gnomad AMR exome AF: 0.0136

Gnomad ASJ exome AF: 0.000165

Gnomad EAS exome AF: 0.0739

Gnomad SAS exome AF: 0.00121

Gnomad FIN exome AF: 0.00387

Gnomad NFE exome AF: 0.000303

Gnomad OTH exome AF: 0.00476

GnomAD4 exome AF: 0.00348 AC: 4937 AN: 1417148 Hom.: 192 Cov.: 32 AF XY: 0.00336 AC XY: 2356 AN XY: 700662

Gnomad4 AFR exome AF: 0.000439

Gnomad4 AMR exome AF: 0.0118

Gnomad4 ASJ exome AF: 0.000524

Gnomad4 EAS exome AF: 0.0927

Gnomad4 SAS exome AF: 0.00144

Gnomad4 FIN exome AF: 0.00313

Gnomad4 NFE exome AF: 0.000220

Gnomad4 OTH exome AF: 0.00495

GnomAD4 genome AF: 0.00427 AC: 650 AN: 152300 Hom.: 15 Cov.: 32 AF XY: 0.00483 AC XY: 360 AN XY: 74470

Gnomad4 AFR AF: 0.000722

Gnomad4 AMR AF: 0.00994

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0727

Gnomad4 SAS AF: 0.00331

Gnomad4 FIN AF: 0.00301

Gnomad4 NFE AF: 0.000456

Gnomad4 OTH AF: 0.00615

Alfa AF: 0.00126 Hom.: 4

Bravo AF: 0.00506

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.7
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2304679; hg19: chr2-27361222; COSMIC: COSV53208585; COSMIC: COSV53208585;