Variant chr2-27138354-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

Variant links:

Genes affected

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

PRR30 links:

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ACMG classification

Classification made for transcript

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 linkuse as main transcript	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 linkuse as main transcript	c.-25C>T		5_prime_UTR_variant	3/3	1	NM_178553.4	P1
PRR30	ENST00000432962.2 linkuse as main transcript	c.-25C>T		5_prime_UTR_variant	3/4	3

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

GnomAD3 exomes

AF:

0.00863

AC:

1846

AN:

213908

Hom.:

AF XY:

0.00753

AC XY:

863

AN XY:

114568

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 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.:

AF XY:

0.00336

AC XY:

2356

AN XY:

700662

show subpopulations

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.:

Cov.:

AF XY:

0.00483

AC XY:

360

AN XY:

74470

show subpopulations

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.:

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over