8-9359476-C-T

Position:

• chr8-9359476-C-T

Variant summary

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

The ENST00000518619.1(PPP1R3B-DT):​n.197-1890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,132 control chromosomes in the GnomAD database, including 59,115 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 0.88 (59115 hom., cov: 31)
• Consequence: PPP1R3B-DT ENST00000518619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

PPP1R3B-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379228	XR_948934.3	n.83+124G>A		intron_variant
LOC105379228	XR_948935.3	n.78+112G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000518619.1	n.197-1890C>T		intron_variant		3
PPP1R3B-DT	ENST00000520255.6	n.740-1890C>T		intron_variant		3
PPP1R3B-DT	ENST00000523246.2	n.1002-1890C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133561 AN: 152014 Hom.: 59087 Cov.: 31

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.878 AC: 133627 AN: 152132 Hom.: 59115 Cov.: 31 AF XY: 0.878 AC XY: 65336 AN XY: 74386

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.920

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.895

Alfa AF: 0.903 Hom.: 10539

Bravo AF: 0.875

Asia WGS AF: 0.901 AC: 3134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.84
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2169384; hg19: chr8-9216986;