rs2304679

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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.141
Variant links:
Genes affected
PRR30 (HGNC:28677): (proline rich 30)

Genome browser will be placed here

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
PRR30NM_178553.4 linkuse as main transcriptc.-25C>T 5_prime_UTR_variant 3/3 ENST00000335524.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PRR30ENST00000335524.7 linkuse as main transcriptc.-25C>T 5_prime_UTR_variant 3/31 NM_178553.4 P1
PRR30ENST00000432962.2 linkuse as main transcriptc.-25C>T 5_prime_UTR_variant 3/43

Frequencies

GnomAD3 genomes
AF:
0.00429
AC:
653
AN:
152182
Hom.:
15
Cov.:
32
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.:
50
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.:
32
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.:
15
Cov.:
32
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.:
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

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

Other links and lift over

dbSNP: rs2304679; hg19: chr2-27361222; COSMIC: COSV53208585; COSMIC: COSV53208585; API