rs12543276

Variant names:

• chr8-9321411-G-A
• rs12543276
• ENST00000520255.6:n.338-4491G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-9321411-G-A
• chr8-9321411-G-C

Variant summary

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

The ENST00000520255.6(PPP1R3B-DT):​n.338-4491G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,154 control chromosomes in the GnomAD database, including 37,190 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 0.68 (37190 hom., cov: 33)
• Consequence: PPP1R3B-DT ENST00000520255.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000520255.6	n.338-4491G>A		intron_variant	Intron 1 of 3	3
PPP1R3B-DT	ENST00000523246.2	n.599+1340G>A		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103935 AN: 152036 Hom.: 37181 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.683 AC: 103982 AN: 152154 Hom.: 37190 Cov.: 33 AF XY: 0.683 AC XY: 50840 AN XY: 74382

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.711

Alfa AF: 0.764 Hom.: 90059

Bravo AF: 0.674

Asia WGS AF: 0.804 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12543276; hg19: chr8-9178921;