chr8-9152396-G-A

Variant names:

• chr8-9152396-G-A
• rs19334
• ENST00000417333.8:n.178+480G>A

Variant summary

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

The ENST00000521718.4(PPP1R3B-DT):​n.233+480G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,056 control chromosomes in the GnomAD database, including 10,650 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 0.35 (10650 hom., cov: 33)
• Consequence: PPP1R3B-DT ENST00000521718.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775
• Publications: 17 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521718.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R3B-DT	NR_183344.1		n.192+480G>A		intron	N/A
	PPP1R3B-DT	NR_183345.1		n.192+480G>A		intron	N/A
	PPP1R3B-DT	NR_183346.1		n.192+480G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R3B-DT	ENST00000417333.8	TSL:5	n.178+480G>A		intron	N/A
	PPP1R3B-DT	ENST00000517816.1	TSL:3	n.125+480G>A		intron	N/A
	PPP1R3B-DT	ENST00000518496.5	TSL:3	n.175+480G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53857 AN: 151938 Hom.: 10619 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.355 AC: 53950 AN: 152056 Hom.: 10650 Cov.: 33 AF XY: 0.362 AC XY: 26945 AN XY: 74334

African (AFR) AF: 0.300 AC: 12434 AN: 41446

American (AMR) AF: 0.528 AC: 8075 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3468

East Asian (EAS) AF: 0.807 AC: 4182 AN: 5180

South Asian (SAS) AF: 0.488 AC: 2351 AN: 4820

European-Finnish (FIN) AF: 0.317 AC: 3352 AN: 10570

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21328 AN: 67976

Other (OTH) AF: 0.379 AC: 798 AN: 2108

Alfa AF: 0.339 Hom.: 35926

Bravo AF: 0.373

Asia WGS AF: 0.609 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.63
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs19334; hg19: chr8-9009906;