8-9320222-T-G

Variant names:

• chr8-9320222-T-G
• rs983309
• ENST00000520255.6:n.338-5680T>G

Variant summary

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

The ENST00000520255.6(PPP1R3B-DT):​n.338-5680T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,238 control chromosomes in the GnomAD database, including 52,867 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 0.83 (52867 hom., cov: 34)
• Consequence: PPP1R3B-DT ENST00000520255.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 42 publications found

Genes affected

PPP1R3B-DT (HGNC:56150): (PPP1R3B divergent transcript)

ENSG00000298955 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520255.6. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R3B-DT	ENST00000520255.6	TSL:3	n.338-5680T>G		intron	N/A
	PPP1R3B-DT	ENST00000523246.2	TSL:5	n.599+151T>G		intron	N/A
	PPP1R3B-DT	ENST00000758838.1		n.130-5680T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126057 AN: 152120 Hom.: 52851 Cov.: 34

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.828 AC: 126124 AN: 152238 Hom.: 52867 Cov.: 34 AF XY: 0.826 AC XY: 61493 AN XY: 74446

African (AFR) AF: 0.708 AC: 29399 AN: 41504

American (AMR) AF: 0.805 AC: 12318 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.926 AC: 3213 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5121 AN: 5188

South Asian (SAS) AF: 0.885 AC: 4275 AN: 4830

European-Finnish (FIN) AF: 0.805 AC: 8535 AN: 10606

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60472 AN: 68020

Other (OTH) AF: 0.836 AC: 1768 AN: 2116

Alfa AF: 0.872 Hom.: 171224

Bravo AF: 0.820

Asia WGS AF: 0.909 AC: 3162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.73
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs983309; hg19: chr8-9177732;