rs10910097

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152371.5(PRXL2B):​c.*564C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 154,398 control chromosomes in the GnomAD database, including 2,451 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 0.17 ( 2415 hom., cov: 33)
Exomes 𝑓: 0.16 ( 36 hom. )

Consequence

PRXL2B
NM_152371.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76
Variant links:
Genes affected
PRXL2B (HGNC:28390): (peroxiredoxin like 2B) Predicted to enable antioxidant activity and prostaglandin-F synthase activity. Predicted to be involved in prostaglandin biosynthetic process. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PRXL2BNM_152371.5 linkuse as main transcriptc.*564C>T 3_prime_UTR_variant 7/7 ENST00000419916.8 NP_689584.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRXL2BENST00000419916.8 linkuse as main transcriptc.*564C>T 3_prime_UTR_variant 7/71 NM_152371.5 ENSP00000394405 P1Q8TBF2-1

Frequencies

GnomAD3 genomes
AF:
0.173
AC:
26261
AN:
152072
Hom.:
2414
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.147
Gnomad AMI
AF:
0.306
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.173
Gnomad EAS
AF:
0.0766
Gnomad SAS
AF:
0.234
Gnomad FIN
AF:
0.200
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.196
Gnomad OTH
AF:
0.190
GnomAD4 exome
AF:
0.162
AC:
357
AN:
2208
Hom.:
36
Cov.:
0
AF XY:
0.170
AC XY:
197
AN XY:
1160
show subpopulations
Gnomad4 AFR exome
AF:
0.208
Gnomad4 AMR exome
AF:
0.0933
Gnomad4 ASJ exome
AF:
0.0758
Gnomad4 EAS exome
AF:
0.139
Gnomad4 SAS exome
AF:
0.133
Gnomad4 FIN exome
AF:
0.172
Gnomad4 NFE exome
AF:
0.176
Gnomad4 OTH exome
AF:
0.144
GnomAD4 genome
AF:
0.173
AC:
26274
AN:
152190
Hom.:
2415
Cov.:
33
AF XY:
0.172
AC XY:
12829
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.147
Gnomad4 AMR
AF:
0.121
Gnomad4 ASJ
AF:
0.173
Gnomad4 EAS
AF:
0.0767
Gnomad4 SAS
AF:
0.234
Gnomad4 FIN
AF:
0.200
Gnomad4 NFE
AF:
0.196
Gnomad4 OTH
AF:
0.189
Alfa
AF:
0.188
Hom.:
2959
Bravo
AF:
0.165
Asia WGS
AF:
0.131
AC:
457
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.4
DANN
Benign
0.69
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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

LitVar

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

Other links and lift over

dbSNP: rs10910097; hg19: chr1-2521430; API