8-9169430-A-G

Variant names:

• chr8-9169430-A-G
• rs365309
• NR_183344.1:n.2162A>G

Variant summary

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

The NR_183344.1(PPP1R3B-DT):​n.2162A>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 0.309 in 151,994 control chromosomes in the GnomAD database, including 8,993 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 0.31 (8993 hom., cov: 32)
• Consequence: PPP1R3B-DT NR_183344.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R3B-DT	NR_183344.1	n.2162A>G		non_coding_transcript_exon_variant	Exon 6 of 6
PPP1R3B-DT	NR_183345.1	n.2162A>G		non_coding_transcript_exon_variant	Exon 6 of 6
PPP1R3B-DT	NR_183346.1	n.2261A>G		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000647722.1	n.375+12583A>G		intron_variant	Intron 3 of 6
PPP1R3B-DT	ENST00000648239.1	n.513+253A>G		intron_variant	Intron 1 of 2
PPP1R3B-DT	ENST00000648278.1	n.274+12583A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46894 AN: 151872 Hom.: 8987 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.309 AC: 46917 AN: 151994 Hom.: 8993 Cov.: 32 AF XY: 0.321 AC XY: 23845 AN XY: 74260

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.351

Alfa AF: 0.319 Hom.: 1400

Bravo AF: 0.312

Asia WGS AF: 0.577 AC: 2002 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	1.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs365309; hg19: chr8-9026940;