2-55626206-T-C

Variant names:

• chr2-55626206-T-C
• rs2627759
• NR_186622.1:n.454-4436T>C

Variant summary

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

The NR_186622.1(PPP4R3B-DT):​n.454-4436T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,944 control chromosomes in the GnomAD database, including 15,965 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 0.44 (15965 hom., cov: 32)
• Consequence: PPP4R3B-DT NR_186622.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806
• Publications: 4 publications found

Genes affected

PPP4R3B-DT (HGNC:55209): (PPP4R3B divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_186622.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP4R3B-DT	NR_186622.1		n.454-4436T>C		intron	N/A
	PPP4R3B-DT	NR_186623.1		n.454-5774T>C		intron	N/A
	PPP4R3B-DT	NR_186624.1		n.454-4436T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67548 AN: 151826 Hom.: 15967 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.445 AC: 67566 AN: 151944 Hom.: 15965 Cov.: 32 AF XY: 0.442 AC XY: 32816 AN XY: 74252

African (AFR) AF: 0.333 AC: 13797 AN: 41400

American (AMR) AF: 0.493 AC: 7525 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3472

East Asian (EAS) AF: 0.109 AC: 563 AN: 5172

South Asian (SAS) AF: 0.268 AC: 1290 AN: 4808

European-Finnish (FIN) AF: 0.563 AC: 5951 AN: 10562

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35410 AN: 67954

Other (OTH) AF: 0.470 AC: 991 AN: 2110

Alfa AF: 0.463 Hom.: 10246

Bravo AF: 0.434

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.6
DANN	Benign	0.67
PhyloP100		0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2627759; hg19: chr2-55853341;