Genetic Variant NM_138333.5:c.*2142A>G (chr9-68783170-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_138333.5(PABIR1):c.*2142A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 166,296 control chromosomes in the GnomAD database, including 1,512 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 0.13 ( 1377 hom., cov: 32)

Exomes 𝑓: 0.13 ( 135 hom. )

Consequence

PABIR1
NM_138333.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.266

Publications

6 publications found

Variant links:

Genes affected

PABIR1 (HGNC:23490): (PP2A Aalpha (PPP2R1A) and B55A (PPP2R2A) interacting phosphatase regulator 1) Enables protein serine/threonine phosphatase inhibitor activity. Involved in mitotic G2/M transition checkpoint; positive regulation of cell growth; and positive regulation of proteasomal ubiquitin-dependent protein catabolic process. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

PABIR1 links:

PIP5K1B (HGNC:8995): (phosphatidylinositol-4-phosphate 5-kinase type 1 beta) Predicted to enable 1-phosphatidylinositol-4-phosphate 5-kinase activity. Predicted to be involved in regulation of phosphatidylinositol 3-kinase signaling. Predicted to act upstream of or within phosphatidylinositol biosynthetic process. Located in uropod. [provided by Alliance of Genome Resources, Apr 2022]

PIP5K1B links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PABIR1	NM_138333.5 link	c.*2142A>G		3_prime_UTR_variant	Exon 1 of 1	ENST00000394264.7	NP_612206.5	Q96E09B3KX07
PIP5K1B	NM_003558.4 link	c.-85-35291A>G		intron_variant	Intron 2 of 15	ENST00000265382.8	NP_003549.1	O14986-1Q7KYT6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PABIR1	ENST00000394264.7 link	c.*2142A>G	3_prime_UTR_variant	Exon 1 of 1	6	NM_138333.5	ENSP00000377807.5	Q96E09
PIP5K1B	ENST00000265382.8 link	c.-85-35291A>G	intron_variant	Intron 2 of 15	1	NM_003558.4	ENSP00000265382.2	O14986-1
PIP5K1B	ENST00000478500.3 link	n.-85-35291A>G	intron_variant	Intron 2 of 20	1		ENSP00000435778.1	O14986-2

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19623

AN:

151302

Hom.:

1380

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.176

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.0837

Gnomad EAS

AF:

0.00175

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.148

GnomAD4 exome

AF:

0.129

AC:

1925

AN:

14878

Hom.:

135

Cov.:

AF XY:

0.128

AC XY:

904

AN XY:

7062

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.129

AC:

1894

AN:

14674

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.219

AC:

AN:

Other (OTH)

AF:

0.106

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

164

247

329

411

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.130

AC:

19622

AN:

151418

Hom.:

1377

Cov.:

AF XY:

0.127

AC XY:

9373

AN XY:

73950

show subpopulations

African (AFR)

AF:

0.101

AC:

4169

AN:

41188

American (AMR)

AF:

0.110

AC:

1674

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.0837

AC:

290

AN:

3466

East Asian (EAS)

AF:

0.00156

AC:

AN:

5126

South Asian (SAS)

AF:

0.106

AC:

511

AN:

4808

European-Finnish (FIN)

AF:

0.136

AC:

1417

AN:

10432

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.163

AC:

11048

AN:

67866

Other (OTH)

AF:

0.146

AC:

308

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

894

1788

2682

3576

4470

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.139

Hom.:

1256

Bravo

AF:

0.122

Asia WGS

AF:

0.0580

AC:

204

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.0

(source)

DANN

Benign

0.44

PhyloP100

-0.27

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.95

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over