dbSNP rs10490413: PAIP2B:c.-11-8889G>A (chr2-71211489-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_020459.1(PAIP2B):c.-11-8889G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,498 control chromosomes in the GnomAD database, including 4,959 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 0.23 ( 4959 hom., cov: 30)

Consequence

PAIP2B
NM_020459.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.169

Publications

4 publications found

Variant links:

Genes affected

PAIP2B (HGNC:29200): (poly(A) binding protein interacting protein 2B) Most mRNAs, except for histones, contain a 3-prime poly(A) tail. Poly(A)-binding protein (PABP; see MIM 604679) enhances translation by circularizing mRNA through its interaction with the translation initiation factor EIF4G1 (MIM 600495) and the poly(A) tail. Various PABP-binding proteins regulate PABP activity, including PAIP1 (MIM 605184), a translational stimulator, and PAIP2A (MIM 605604) and PAIP2B, translational inhibitors (Derry et al., 2006 [PubMed 17381337]).[supplied by OMIM, Mar 2008]

PAIP2B links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_020459.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020459.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAIP2B	NM_020459.1	MANE Select	c.-11-8889G>A		intron	N/A	NP_065192.1	Q9ULR5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PAIP2B	ENST00000244221.9	TSL:1 MANE Select	c.-11-8889G>A	intron	N/A	ENSP00000244221.8	Q9ULR5
PAIP2B	ENST00000890279.1		c.-11-8889G>A	intron	N/A	ENSP00000560339.1
PAIP2B	ENST00000890282.1		c.-11-8889G>A	intron	N/A	ENSP00000560341.1

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35535

AN:

151374

Hom.:

4952

Cov.:

show subpopulations

Gnomad AFR

AF:

0.382

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.00194

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.230

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.235

AC:

35562

AN:

151498

Hom.:

4959

Cov.:

AF XY:

0.231

AC XY:

17054

AN XY:

73958

show subpopulations

African (AFR)

AF:

0.381

AC:

15746

AN:

41280

American (AMR)

AF:

0.153

AC:

2326

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

676

AN:

3466

East Asian (EAS)

AF:

0.00194

AC:

AN:

5150

South Asian (SAS)

AF:

0.122

AC:

588

AN:

4806

European-Finnish (FIN)

AF:

0.238

AC:

2476

AN:

10400

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.192

AC:

13013

AN:

67866

Other (OTH)

AF:

0.227

AC:

478

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1278

2556

3833

5111

6389

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.220

Hom.:

688

Bravo

AF:

0.237

Asia WGS

AF:

0.0770

AC:

272

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.1

(source)

DANN

Benign

0.63

PhyloP100

-0.17

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over