chr2-55579177-C-T

Variant names:

• chr2-55579177-C-T
• rs10496050
• NM_001122964.3:c.1468+502G>A

Variant summary

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

The NM_001122964.3(PPP4R3B):​c.1468+502G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,886 control chromosomes in the GnomAD database, including 16,060 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 (16060 hom., cov: 32)
• Consequence: PPP4R3B NM_001122964.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 7 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP4R3B	NM_001122964.3	c.1468+502G>A		intron_variant	Intron 9 of 16	ENST00000616407.2	NP_001116436.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP4R3B	ENST00000616407.2	c.1468+502G>A		intron_variant	Intron 9 of 16	1	NM_001122964.3	ENSP00000483228.1
PPP4R3B	ENST00000616288.4	c.1468+502G>A		intron_variant	Intron 9 of 15	1		ENSP00000484116.1
PPP4R3B	ENST00000611717.4	c.1468+502G>A		intron_variant	Intron 9 of 14	1		ENSP00000478677.1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67926 AN: 151766 Hom.: 16061 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.447 AC: 67950 AN: 151886 Hom.: 16060 Cov.: 32 AF XY: 0.445 AC XY: 33055 AN XY: 74216

African (AFR) AF: 0.330 AC: 13668 AN: 41450

American (AMR) AF: 0.498 AC: 7605 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1609 AN: 3470

East Asian (EAS) AF: 0.172 AC: 892 AN: 5182

South Asian (SAS) AF: 0.269 AC: 1295 AN: 4812

European-Finnish (FIN) AF: 0.565 AC: 5950 AN: 10538

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35505 AN: 67862

Other (OTH) AF: 0.476 AC: 1005 AN: 2110

Alfa AF: 0.467 Hom.: 10261

Bravo AF: 0.437

Asia WGS AF: 0.276 AC: 960 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.028
DANN	Benign	0.61
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: rs10496050; hg19: chr2-55806313;