8-9325848-A-G

Position:

• chr8-9325848-A-G

Variant summary

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

The ENST00000647924.1(PPP1R3B-DT):​n.14A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,282 control chromosomes in the GnomAD database, including 58,460 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 0.87 (58451 hom., cov: 33)
  • Exomes 𝑓: 1.0 (9 hom.)
• Consequence: PPP1R3B-DT ENST00000647924.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

Genes affected

PPP1R3B-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC157273	NR_040039.1	n.364-54A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000647924.1	n.14A>G		non_coding_transcript_exon_variant	1/5
PPP1R3B-DT	ENST00000520255.6	n.338-54A>G		intron_variant		3
PPP1R3B-DT	ENST00000520390.1	n.364-54A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.874 AC: 133032 AN: 152146 Hom.: 58432 Cov.: 33

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.880

GnomAD4 exome AF: 1.00 AC: 18 AN: 18 Hom.: 9 AF XY: 1.00 AC XY: 12 AN XY: 12

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.874 AC: 133109 AN: 152264 Hom.: 58451 Cov.: 33 AF XY: 0.871 AC XY: 64819 AN XY: 74448

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.876

Alfa AF: 0.908 Hom.: 12920

Bravo AF: 0.868

Asia WGS AF: 0.918 AC: 3195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9987289; hg19: chr8-9183358;