8-9320758-A-T

Position:

• chr8-9320758-A-T

Variant summary

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

The ENST00000523246.2(PPP1R3B-DT):​n.599+687A>T 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 0.856 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 ENST00000523246.2 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R3B-DT	ENST00000523246.2	n.599+687A>T		intron_variant, non_coding_transcript_variant		5
PPP1R3B-DT	ENST00000520255.6	n.338-5144A>T		intron_variant, non_coding_transcript_variant		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

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;