rs19334

chr8-9152396-G-Achr8-9152396-G-Cchr8-9152396-G-T

Variant summary

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

The NR_183345.1(PPP1R3B-DT):n.192+480G>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 0.355 in 152,056 control chromosomes in the GnomAD database, including 10,650 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 0.35 (10650 hom., cov: 33)
• Consequence: PPP1R3B-DT NR_183345.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP1R3B-DT	NR_183345.1	n.192+480G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R3B-DT	ENST00000517816.1	n.125+480G>A		intron_variant, non_coding_transcript_variant		3
PPP1R3B-DT	ENST00000518496.5	n.175+480G>A		intron_variant, non_coding_transcript_variant		3
PPP1R3B-DT	ENST00000521718.3	n.221+480G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53857 AN: 151938 Hom.: 10619 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.355 AC: 53950 AN: 152056 Hom.: 10650 Cov.: 33 AF XY: 0.362 AC XY: 26945 AN XY: 74334

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.379

Alfa AF: 0.339 Hom.: 14992

Bravo AF: 0.373

Asia WGS AF: 0.609 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.5
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs19334; hg19: chr8-9009906;