9-68783170-A-G

Variant names:

• chr9-68783170-A-G
• rs12006032
• NM_138333.5:c.*2142A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 6 publications found

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]

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138333.5. 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
	PABIR1	NM_138333.5	MANE Select	c.*2142A>G		3_prime_UTR	Exon 1 of 1	NP_612206.5
	PIP5K1B	NM_003558.4	MANE Select	c.-85-35291A>G		intron	N/A	NP_003549.1	O14986-1
	PIP5K1B	NM_001376036.1		c.-85-35291A>G		intron	N/A	NP_001362965.1	O14986-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PABIR1	ENST00000394264.7	TSL:6 MANE Select	c.*2142A>G		3_prime_UTR	Exon 1 of 1	ENSP00000377807.5	Q96E09
	PIP5K1B	ENST00000265382.8	TSL:1 MANE Select	c.-85-35291A>G		intron	N/A	ENSP00000265382.2	O14986-1
	PIP5K1B	ENST00000478500.3	TSL:1	n.-85-35291A>G		intron	N/A	ENSP00000435778.1	O14986-2

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19623 AN: 151302 Hom.: 1380 Cov.: 32

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.: 0 AF XY: 0.128 AC XY: 904 AN XY: 7062

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.129 AC: 1894 AN: 14674

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.219 AC: 21 AN: 96

Other (OTH) AF: 0.106 AC: 10 AN: 94

GnomAD4 genome AF: 0.130 AC: 19622 AN: 151418 Hom.: 1377 Cov.: 32 AF XY: 0.127 AC XY: 9373 AN XY: 73950

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: 8 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: 37 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11048 AN: 67866

Other (OTH) AF: 0.146 AC: 308 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
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)

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

Other links and lift over

dbSNP: rs12006032; hg19: chr9-71398086;