8-9326721-G-A

Variant names:

• chr8-9326721-G-A
• rs4240624
• ENST00000518619.1:n.196+418G>A

Variant summary

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

The ENST00000520390.1(PPP1R3B-DT):​n.765+418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,220 control chromosomes in the GnomAD database, including 58,414 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 0.87 (58414 hom., cov: 33)
• Consequence: PPP1R3B-DT ENST00000520390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 111 publications found

Genes affected

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

LOC157273 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• 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: ENST00000520390.1. 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
	LOC157273	NR_040039.1		n.765+418G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R3B-DT	ENST00000518619.1	TSL:3	n.196+418G>A		intron	N/A
	PPP1R3B-DT	ENST00000520255.6	TSL:3	n.739+418G>A		intron	N/A
	PPP1R3B-DT	ENST00000520390.1	TSL:2	n.765+418G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132976 AN: 152102 Hom.: 58394 Cov.: 33

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.874 AC: 133054 AN: 152220 Hom.: 58414 Cov.: 33 AF XY: 0.871 AC XY: 64788 AN XY: 74414

African (AFR) AF: 0.812 AC: 33710 AN: 41538

American (AMR) AF: 0.829 AC: 12660 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3276 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5122 AN: 5186

South Asian (SAS) AF: 0.892 AC: 4298 AN: 4820

European-Finnish (FIN) AF: 0.839 AC: 8874 AN: 10582

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62080 AN: 68020

Other (OTH) AF: 0.876 AC: 1853 AN: 2116

Alfa AF: 0.871 Hom.: 16467

Bravo AF: 0.867

Asia WGS AF: 0.919 AC: 3196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.65
DANN	Benign	0.62
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4240624; hg19: chr8-9184231;