chr2-55623128-A-G

Variant names:

• chr2-55623128-A-G
• rs782603
• ENST00000749892.1:n.495-2593A>G

Variant summary

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

The ENST00000749892.1(PPP4R3B-DT):​n.495-2593A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.933 in 152,250 control chromosomes in the GnomAD database, including 66,835 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 0.93 (66835 hom., cov: 31)
• Consequence: PPP4R3B-DT ENST00000749892.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP4R3B-DT	NR_186621.1	n.454-2593A>G		intron_variant	Intron 1 of 1
PPP4R3B-DT	NR_186622.1	n.453+4746A>G		intron_variant	Intron 1 of 1
PPP4R3B-DT	NR_186623.1	n.453+4746A>G		intron_variant	Intron 1 of 1
PPP4R3B-DT	NR_186624.1	n.453+4746A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP4R3B-DT	ENST00000749892.1	n.495-2593A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.933 AC: 141932 AN: 152132 Hom.: 66793 Cov.: 31

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.866

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.933 AC: 142027 AN: 152250 Hom.: 66835 Cov.: 31 AF XY: 0.929 AC XY: 69147 AN XY: 74432

African (AFR) AF: 0.977 AC: 40599 AN: 41550

American (AMR) AF: 0.932 AC: 14254 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3197 AN: 3472

East Asian (EAS) AF: 0.509 AC: 2627 AN: 5164

South Asian (SAS) AF: 0.820 AC: 3955 AN: 4826

European-Finnish (FIN) AF: 0.965 AC: 10222 AN: 10596

Middle Eastern (MID) AF: 0.866 AC: 253 AN: 292

European-Non Finnish (NFE) AF: 0.943 AC: 64163 AN: 68024

Other (OTH) AF: 0.911 AC: 1926 AN: 2114

Alfa AF: 0.946 Hom.: 8476

Bravo AF: 0.932

Asia WGS AF: 0.682 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs782603; hg19: chr2-55850263;