NM_001300783.2:c.160-83958G>A

Variant summary

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

The NM_001300783.2(PRR16):​c.160-83958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0913 in 152,018 control chromosomes in the GnomAD database, including 1,359 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 0.091 ( 1359 hom., cov: 32)

Consequence

PRR16
NM_001300783.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.229

Publications

5 publications found
Variant links:
Genes affected
PRR16 (HGNC:29654): (proline rich 16) Involved in positive regulation of cell size and positive regulation of translation. [provided by Alliance of Genome Resources, Apr 2022]

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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PRR16NM_001300783.2 linkc.160-83958G>A intron_variant Intron 1 of 1 ENST00000407149.7 NP_001287712.1 Q569H4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PRR16ENST00000407149.7 linkc.160-83958G>A intron_variant Intron 1 of 1 1 NM_001300783.2 ENSP00000385118.2 Q569H4-1
PRR16ENST00000379551.2 linkc.91-83958G>A intron_variant Intron 2 of 2 1 ENSP00000368869.2 Q569H4-3
PRR16ENST00000505123.5 linkc.-273-15099G>A intron_variant Intron 1 of 3 3 ENSP00000423446.1 Q569H4-2
PRR16ENST00000509923.1 linkc.-51-83958G>A intron_variant Intron 1 of 1 3 ENSP00000421256.1 D6RGF0

Frequencies

GnomAD3 genomes
AF:
0.0911
AC:
13844
AN:
151902
Hom.:
1356
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.252
Gnomad AMI
AF:
0.0197
Gnomad AMR
AF:
0.0436
Gnomad ASJ
AF:
0.0395
Gnomad EAS
AF:
0.000771
Gnomad SAS
AF:
0.0338
Gnomad FIN
AF:
0.0493
Gnomad MID
AF:
0.0696
Gnomad NFE
AF:
0.0260
Gnomad OTH
AF:
0.0651
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0913
AC:
13875
AN:
152018
Hom.:
1359
Cov.:
32
AF XY:
0.0892
AC XY:
6633
AN XY:
74332
show subpopulations
African (AFR)
AF:
0.252
AC:
10444
AN:
41454
American (AMR)
AF:
0.0435
AC:
664
AN:
15248
Ashkenazi Jewish (ASJ)
AF:
0.0395
AC:
137
AN:
3468
East Asian (EAS)
AF:
0.000772
AC:
4
AN:
5178
South Asian (SAS)
AF:
0.0340
AC:
164
AN:
4822
European-Finnish (FIN)
AF:
0.0493
AC:
523
AN:
10612
Middle Eastern (MID)
AF:
0.0680
AC:
20
AN:
294
European-Non Finnish (NFE)
AF:
0.0260
AC:
1765
AN:
67918
Other (OTH)
AF:
0.0644
AC:
136
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
565
1130
1695
2260
2825
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
136
272
408
544
680
<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:
0.0471
Hom.:
1630
Bravo
AF:
0.0984
Asia WGS
AF:
0.0250
AC:
87
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.0
DANN
Benign
0.20
PhyloP100
0.23
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

Publications

Other links and lift over

dbSNP: rs1584468; hg19: chr5-119937691; API