NM_001122964.3:c.198+947A>G

Variant names:

• chr2-55614504-T-C
• rs782588
• NM_001122964.3:c.198+947A>G

Variant summary

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

The NM_001122964.3(PPP4R3B):​c.198+947A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,036 control chromosomes in the GnomAD database, including 16,250 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 0.45 (16250 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: PPP4R3B NM_001122964.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 6 publications found

Genes affected

PPP4R3B (HGNC:29267): (protein phosphatase 4 regulatory subunit 3B) Predicted to act upstream of or within positive regulation of gluconeogenesis and protein dephosphorylation. Located in centrosome and nuclear speck. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP4R3B	NM_001122964.3	c.198+947A>G		intron_variant	Intron 2 of 16	ENST00000616407.2	NP_001116436.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP4R3B	ENST00000616407.2	c.198+947A>G		intron_variant	Intron 2 of 16	1	NM_001122964.3	ENSP00000483228.1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68337 AN: 151918 Hom.: 16250 Cov.: 34

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.478

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.450 AC: 68358 AN: 152036 Hom.: 16250 Cov.: 34 AF XY: 0.447 AC XY: 33233 AN XY: 74334

African (AFR) AF: 0.348 AC: 14437 AN: 41486

American (AMR) AF: 0.496 AC: 7575 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3470

East Asian (EAS) AF: 0.109 AC: 568 AN: 5190

South Asian (SAS) AF: 0.262 AC: 1265 AN: 4826

European-Finnish (FIN) AF: 0.577 AC: 6092 AN: 10558

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35381 AN: 67908

Other (OTH) AF: 0.475 AC: 1002 AN: 2110

Alfa AF: 0.468 Hom.: 10458

Bravo AF: 0.440

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.71
DANN	Benign	0.53
PhyloP100		-2.3

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: rs782588; hg19: chr2-55841640;