dbSNP rs10910097: PRXL2B:n.1029C>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 ENST00000476686.1(PRXL2B):n.1029C>T variant causes a non coding transcript exon 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
ENST00000476686.1 non_coding_transcript_exon

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRXL2B	NM_152371.5 link	c.*564C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000419916.8	NP_689584.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRXL2B	ENST00000419916.8 link	c.*564C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_152371.5	ENSP00000394405.4		Q8TBF2-1

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 v4.3

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over