rs1530483

Variant names:

• chr8-9170751-C-A
• rs1530483
• ENST00000647722.1:n.375+13904C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647722.1(PPP1R3B-DT):​n.375+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 ENST00000647722.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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	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
PPP1R3B-DT	ENST00000648278.1	n.274+13904C>A		intron_variant	Intron 3 of 5

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

Gnomad4 AFR AF: 0.0286

Gnomad4 AMR AF: 0.0863

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0701

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.118

Alfa AF: 0.150 Hom.: 1868

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1530483; hg19: chr8-9028261;