8-9359476-C-T

Variant names:

• chr8-9359476-C-T
• rs2169384
• ENST00000759801.1:n.487G>A

Variant summary

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

The ENST00000759801.1(ENSG00000254237):​n.487G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,132 control chromosomes in the GnomAD database, including 59,115 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 0.88 (59115 hom., cov: 31)
• Consequence: ENSG00000254237 ENST00000759801.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 4 publications found

Genes affected

ENSG00000254237 (HGNC:):

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

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 = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379228	XR_948934.3	n.83+124G>A		intron_variant	Intron 1 of 2
LOC105379228	XR_948935.3	n.78+112G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254237	ENST00000759801.1	n.487G>A		non_coding_transcript_exon_variant	Exon 2 of 2
PPP1R3B-DT	ENST00000518619.1	n.197-1890C>T		intron_variant	Intron 1 of 3	3
PPP1R3B-DT	ENST00000520255.6	n.740-1890C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133561 AN: 152014 Hom.: 59087 Cov.: 31

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.878 AC: 133627 AN: 152132 Hom.: 59115 Cov.: 31 AF XY: 0.878 AC XY: 65336 AN XY: 74386

African (AFR) AF: 0.763 AC: 31648 AN: 41472

American (AMR) AF: 0.916 AC: 13996 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3139 AN: 3468

East Asian (EAS) AF: 0.943 AC: 4873 AN: 5168

South Asian (SAS) AF: 0.878 AC: 4228 AN: 4814

European-Finnish (FIN) AF: 0.920 AC: 9759 AN: 10602

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63023 AN: 68004

Other (OTH) AF: 0.895 AC: 1892 AN: 2114

Alfa AF: 0.903 Hom.: 10539

Bravo AF: 0.875

Asia WGS AF: 0.901 AC: 3134 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	0.84
DANN	Benign	0.48
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs2169384; hg19: chr8-9216986;