8-9320758-A-T

Variant names:

• chr8-9320758-A-T
• rs6984305
• ENST00000520255.6:n.338-5144A>T

Variant summary

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

The ENST00000520255.6(PPP1R3B-DT):​n.338-5144A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,248 control chromosomes in the GnomAD database, including 56,101 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 0.86 (56101 hom., cov: 33)
• Consequence: PPP1R3B-DT ENST00000520255.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395

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 (EAS) allele frequency at 95% confidence interval = 0.964 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	ENST00000520255.6	n.338-5144A>T		intron_variant	Intron 1 of 3	3
PPP1R3B-DT	ENST00000523246.2	n.599+687A>T		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130254 AN: 152130 Hom.: 56081 Cov.: 33

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.856 AC: 130331 AN: 152248 Hom.: 56101 Cov.: 33 AF XY: 0.853 AC XY: 63473 AN XY: 74440

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.937

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.860

Alfa AF: 0.892 Hom.: 33566

Bravo AF: 0.849

Asia WGS AF: 0.915 AC: 3184 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	4.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6984305; hg19: chr8-9178268;