rs1530483

Variant names:

• chr8-9170751-C-A
• rs1530483
• ENST00000417333.8:n.408+13904C>A

Variant summary

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

The ENST00000417333.8(PPP1R3B-DT):​n.408+13904C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,180 control chromosomes in the GnomAD database, including 1,225 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 0.11 (1225 hom., cov: 32)
• Consequence: PPP1R3B-DT ENST00000417333.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000417333.8	n.408+13904C>A		intron_variant	Intron 3 of 5	5
PPP1R3B-DT	ENST00000647722.1	n.375+13904C>A		intron_variant	Intron 3 of 6
PPP1R3B-DT	ENST00000648239.1	n.513+1574C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16975 AN: 152062 Hom.: 1225 Cov.: 32

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.112 AC: 16968 AN: 152180 Hom.: 1225 Cov.: 32 AF XY: 0.109 AC XY: 8134 AN XY: 74398

African (AFR) AF: 0.0286 AC: 1189 AN: 41550

American (AMR) AF: 0.0863 AC: 1319 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3472

East Asian (EAS) AF: 0.0701 AC: 363 AN: 5182

South Asian (SAS) AF: 0.177 AC: 854 AN: 4818

European-Finnish (FIN) AF: 0.131 AC: 1392 AN: 10592

Middle Eastern (MID) AF: 0.155 AC: 45 AN: 290

European-Non Finnish (NFE) AF: 0.157 AC: 10674 AN: 67978

Other (OTH) AF: 0.118 AC: 248 AN: 2100

Alfa AF: 0.134 Hom.: 2457

Bravo AF: 0.101

Asia WGS AF: 0.128 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.50
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1530483; hg19: chr8-9028261;