dbSNP rs10910097: PRXL2B:c.*564C>T (chr1-2589991-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

Publications

12 publications found

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]

PRXL2B 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=-0.9).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152371.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PRXL2B	NM_152371.5	MANE Select	c.*564C>T	3_prime_UTR	Exon 7 of 7	NP_689584.5
PRXL2B	NM_001195736.3		c.*564C>T	3_prime_UTR	Exon 7 of 7	NP_001182665.4
PRXL2B	NM_001195737.3		c.*564C>T	3_prime_UTR	Exon 7 of 7	NP_001182666.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PRXL2B	ENST00000419916.8	TSL:1 MANE Select	c.*564C>T	3_prime_UTR	Exon 7 of 7	ENSP00000394405.4	Q8TBF2-1
PRXL2B	ENST00000476686.1	TSL:1	n.1029C>T	non_coding_transcript_exon	Exon 2 of 2
PRXL2B	ENST00000444521.6	TSL:2	c.*564C>T	3_prime_UTR	Exon 7 of 7	ENSP00000413218.3	A0A0A0MT35

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26261

AN:

152072

Hom.:

2414

Cov.:

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.:

Cov.:

AF XY:

0.170

AC XY:

197

AN XY:

1160

show subpopulations

African (AFR)

AF:

0.208

AC:

AN:

American (AMR)

AF:

0.0933

AC:

AN:

150

Ashkenazi Jewish (ASJ)

AF:

0.0758

AC:

AN:

East Asian (EAS)

AF:

0.139

AC:

AN:

122

South Asian (SAS)

AF:

0.133

AC:

AN:

158

European-Finnish (FIN)

AF:

0.172

AC:

AN:

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.176

AC:

264

AN:

1498

Other (OTH)

AF:

0.144

AC:

AN:

104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome 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

GnomAD4 genome

AF:

0.173

AC:

26274

AN:

152190

Hom.:

2415

Cov.:

AF XY:

0.172

AC XY:

12829

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.147

AC:

6098

AN:

41526

American (AMR)

AF:

0.121

AC:

1856

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

600

AN:

3470

East Asian (EAS)

AF:

0.0767

AC:

397

AN:

5174

South Asian (SAS)

AF:

0.234

AC:

1130

AN:

4822

European-Finnish (FIN)

AF:

0.200

AC:

2119

AN:

10596

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.196

AC:

13334

AN:

67986

Other (OTH)

AF:

0.189

AC:

400

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1134

2268

3401

4535

5669

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

312

624

936

1248

1560

<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:

0.184

Hom.:

4128

Bravo

AF:

0.165

Asia WGS

AF:

0.131

AC:

457

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

(source)

DANN

Benign

0.69

PhyloP100

-1.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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