ENST00000520255.6:n.338-4491G>A

Variant names:

• chr8-9321411-G-A
• rs12543276
• ENST00000520255.6:n.338-4491G>A

Variant summary

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

The ENST00000520255.6(PPP1R3B-DT):​n.338-4491G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,154 control chromosomes in the GnomAD database, including 37,190 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 0.68 (37190 hom., cov: 33)
• Consequence: PPP1R3B-DT ENST00000520255.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 11 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 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.338-4491G>A		intron	N/A
	PPP1R3B-DT	ENST00000523246.2	TSL:5	n.599+1340G>A		intron	N/A
	PPP1R3B-DT	ENST00000758838.1		n.130-4491G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103935 AN: 152036 Hom.: 37181 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.683 AC: 103982 AN: 152154 Hom.: 37190 Cov.: 33 AF XY: 0.683 AC XY: 50840 AN XY: 74382

African (AFR) AF: 0.466 AC: 19349 AN: 41482

American (AMR) AF: 0.713 AC: 10912 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2801 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5062 AN: 5176

South Asian (SAS) AF: 0.702 AC: 3382 AN: 4818

European-Finnish (FIN) AF: 0.709 AC: 7499 AN: 10576

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52612 AN: 68012

Other (OTH) AF: 0.711 AC: 1505 AN: 2116

Alfa AF: 0.751 Hom.: 190173

Bravo AF: 0.674

Asia WGS AF: 0.804 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs12543276; hg19: chr8-9178921;