rs4240624

Positions:

• chr8-9326721-G-A
• chr8-9326721-G-C

Variant summary

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

The ENST00000520390.1(PPP1R3B-DT):​n.765+418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,220 control chromosomes in the GnomAD database, including 58,414 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 (58414 hom., cov: 33)
• Consequence: PPP1R3B-DT ENST00000520390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

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

LOC157273 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• 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/exons	MANE	Protein	UniProt
LOC157273	NR_040039.1	n.765+418G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000518619.1	n.196+418G>A		intron_variant		3
PPP1R3B-DT	ENST00000520255.6	n.739+418G>A		intron_variant		3
PPP1R3B-DT	ENST00000520390.1	n.765+418G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132976 AN: 152102 Hom.: 58394 Cov.: 33

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.874 AC: 133054 AN: 152220 Hom.: 58414 Cov.: 33 AF XY: 0.871 AC XY: 64788 AN XY: 74414

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.876

Alfa AF: 0.893 Hom.: 7559

Bravo AF: 0.867

Asia WGS AF: 0.919 AC: 3196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.65
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4240624; hg19: chr8-9184231;