rs13265179

Positions:

• chr8-9337184-C-A
• chr8-9337184-C-G
• chr8-9337184-C-T

Variant summary

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

The ENST00000523246.2(PPP1R3B-DT):​n.1001+10881C>A 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 0.0992 in 152,226 control chromosomes in the GnomAD database, including 1,114 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 0.099 (1114 hom., cov: 33)
• Consequence: PPP1R3B-DT ENST00000523246.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 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.1001+10881C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0992 AC: 15085 AN: 152108 Hom.: 1109 Cov.: 33

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0739

Gnomad EAS AF: 0.00967

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0991

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

GnomAD4 genome AF: 0.0992 AC: 15103 AN: 152226 Hom.: 1114 Cov.: 33 AF XY: 0.104 AC XY: 7761 AN XY: 74414

Gnomad4 AFR AF: 0.0318

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.0739

Gnomad4 EAS AF: 0.00969

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0337 Hom.: 27

Bravo AF: 0.102

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13265179; hg19: chr8-9194694;