rs1530483

Positions:

• chr8-9170751-C-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000647722.1	n.375+13904C>A		intron_variant, non_coding_transcript_variant
PPP1R3B-DT	ENST00000648239.1	n.513+1574C>A		intron_variant, non_coding_transcript_variant
PPP1R3B-DT	ENST00000648278.1	n.274+13904C>A		intron_variant, non_coding_transcript_variant

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;