rs10099338

Variant names:

• chr8-9400229-A-G
• rs10099338
• ENST00000520255.6:n.798-13420A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520255.6(PPP1R3B-DT):​n.798-13420A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,180 control chromosomes in the GnomAD database, including 2,573 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 0.16 (2573 hom., cov: 32)
• Consequence: PPP1R3B-DT ENST00000520255.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 0 publications found

Genes affected

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

ENSG00000254237 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520255.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R3B-DT	ENST00000520255.6	TSL:3	n.798-13420A>G		intron	N/A
	ENSG00000254237	ENST00000521842.3	TSL:3	n.208+3716T>C		intron	N/A
	ENSG00000254237	ENST00000522129.5	TSL:4	n.175-16229T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24223 AN: 152062 Hom.: 2570 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.159 AC: 24236 AN: 152180 Hom.: 2573 Cov.: 32 AF XY: 0.154 AC XY: 11482 AN XY: 74416

African (AFR) AF: 0.298 AC: 12338 AN: 41454

American (AMR) AF: 0.111 AC: 1691 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3470

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5182

South Asian (SAS) AF: 0.0671 AC: 324 AN: 4826

European-Finnish (FIN) AF: 0.0913 AC: 969 AN: 10612

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7775 AN: 68018

Other (OTH) AF: 0.162 AC: 342 AN: 2112

Alfa AF: 0.125 Hom.: 810

Bravo AF: 0.165

Asia WGS AF: 0.0670 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10099338;

hg19: chr8-9257739;