8-9327636-T-C

Variant names:

• chr8-9327636-T-C
• rs2126259
• ENST00000518619.1:n.196+1333T>C

Variant summary

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

The ENST00000518619.1(PPP1R3B-DT):​n.196+1333T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,198 control chromosomes in the GnomAD database, including 57,732 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 0.87 (57732 hom., cov: 32)
• Consequence: PPP1R3B-DT ENST00000518619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 73 publications found

Genes affected

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

LOC157273 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC157273	NR_040039.1	n.765+1333T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000518619.1	n.196+1333T>C		intron_variant	Intron 1 of 3	3
PPP1R3B-DT	ENST00000520255.6	n.739+1333T>C		intron_variant	Intron 2 of 3	3
PPP1R3B-DT	ENST00000520390.1	n.765+1333T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132161 AN: 152082 Hom.: 57710 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.869 AC: 132235 AN: 152198 Hom.: 57732 Cov.: 32 AF XY: 0.865 AC XY: 64347 AN XY: 74420

African (AFR) AF: 0.832 AC: 34529 AN: 41510

American (AMR) AF: 0.785 AC: 11991 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3265 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5120 AN: 5186

South Asian (SAS) AF: 0.888 AC: 4289 AN: 4828

European-Finnish (FIN) AF: 0.823 AC: 8708 AN: 10584

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61352 AN: 68014

Other (OTH) AF: 0.869 AC: 1837 AN: 2114

Alfa AF: 0.895 Hom.: 206491

Bravo AF: 0.861

Asia WGS AF: 0.919 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2126259; hg19: chr8-9185146;