rs10099338

Positions:

• chr8-9400229-A-G

Variant summary

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

The ENST00000522129.5(ENSG00000254237):​n.175-16229T>C 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 0.159 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: ENST00000522129.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379231	XR_002956685.1	n.99-3634A>G		intron_variant, non_coding_transcript_variant
LOC105379231	XR_948940.3	n.99-3634A>G		intron_variant, non_coding_transcript_variant
LOC105379231	XR_948941.3	n.99-13420A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000522129.5	n.175-16229T>C		intron_variant, non_coding_transcript_variant		4
PPP1R3B-DT	ENST00000523246.2	n.1060-3634A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.0671

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.162

Alfa AF: 0.125 Hom.: 758

Bravo AF: 0.165

Asia WGS AF: 0.0670 AC: 234 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	3.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10099338; hg19: chr8-9257739;