8-9320758-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 31 publications found

Genes affected

PPP1R3B-DT (HGNC:56150): (PPP1R3B divergent transcript)

ENSG00000298955 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
PPP1R3B-DT	ENST00000758838.1	n.130-5144A>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.789 AC: 32786 AN: 41532

American (AMR) AF: 0.819 AC: 12525 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3253 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5111 AN: 5178

South Asian (SAS) AF: 0.888 AC: 4283 AN: 4824

European-Finnish (FIN) AF: 0.817 AC: 8662 AN: 10604

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60774 AN: 68026

Other (OTH) AF: 0.860 AC: 1819 AN: 2114

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
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs6984305; hg19: chr8-9178268;