dbSNP rs2304679: PRR30:c.-25C>T (chr2-27138354-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.141

Publications

2 publications found

Variant links:

Genes affected

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

PRR30 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178553.4. 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
	PRR30	NM_178553.4	MANE Select	c.-25C>T		5_prime_UTR	Exon 3 of 3	NP_848648.2	Q53SZ7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR30	ENST00000335524.7	TSL:1 MANE Select	c.-25C>T		5_prime_UTR	Exon 3 of 3	ENSP00000335017.3	Q53SZ7
	PRR30	ENST00000432962.2	TSL:3	c.-25C>T		5_prime_UTR	Exon 3 of 4	ENSP00000393468.2	C9JVA3

Frequencies

GnomAD3 genomes

AF:

0.00429

AC:

653

AN:

152182

Hom.:

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.00863

AC:

1846

AN:

213908

AF XY:

0.00753

show subpopulations

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 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.:

AF XY:

0.00336

AC XY:

2356

AN XY:

700662

show subpopulations

African (AFR)

AF:

0.000439

AC:

AN:

31912

American (AMR)

AF:

0.0118

AC:

461

AN:

39068

Ashkenazi Jewish (ASJ)

AF:

0.000524

AC:

AN:

22880

East Asian (EAS)

AF:

0.0927

AC:

3643

AN:

39316

South Asian (SAS)

AF:

0.00144

AC:

115

AN:

79770

European-Finnish (FIN)

AF:

0.00313

AC:

162

AN:

51702

Middle Eastern (MID)

AF:

0.000511

AC:

AN:

3914

European-Non Finnish (NFE)

AF:

0.000220

AC:

240

AN:

1090376

Other (OTH)

AF:

0.00495

AC:

288

AN:

58210

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

287

574

862

1149

1436

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

192

256

320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00427

AC:

650

AN:

152300

Hom.:

Cov.:

AF XY:

0.00483

AC XY:

360

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.000722

AC:

AN:

41564

American (AMR)

AF:

0.00994

AC:

152

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.0727

AC:

376

AN:

5172

South Asian (SAS)

AF:

0.00331

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00301

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000456

AC:

AN:

68028

Other (OTH)

AF:

0.00615

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

129

161

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00159

Hom.:

Bravo

AF:

0.00506

Asia WGS

AF:

0.0330

AC:

113

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.7

(source)

DANN

Benign

0.71

PhyloP100

-0.14

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over