rs13265179

Variant names:

• chr8-9337184-C-A
• rs13265179
• ENST00000518619.1:n.196+10881C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-9337184-C-A
• chr8-9337184-C-G
• chr8-9337184-C-T

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+10881C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0992 in 152,226 control chromosomes in the GnomAD database, including 1,114 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 0.099 (1114 hom., cov: 33)
• Consequence: PPP1R3B-DT ENST00000518619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311
• Publications: 2 publications found

Genes affected

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 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	ENST00000518619.1	n.196+10881C>A		intron_variant	Intron 1 of 3	3
PPP1R3B-DT	ENST00000520255.6	n.739+10881C>A		intron_variant	Intron 2 of 3	3
PPP1R3B-DT	ENST00000523246.2	n.1001+10881C>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0992 AC: 15085 AN: 152108 Hom.: 1109 Cov.: 33

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0739

Gnomad EAS AF: 0.00967

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0991

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

GnomAD4 genome AF: 0.0992 AC: 15103 AN: 152226 Hom.: 1114 Cov.: 33 AF XY: 0.104 AC XY: 7761 AN XY: 74414

African (AFR) AF: 0.0318 AC: 1322 AN: 41570

American (AMR) AF: 0.215 AC: 3283 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0739 AC: 256 AN: 3462

East Asian (EAS) AF: 0.00969 AC: 50 AN: 5160

South Asian (SAS) AF: 0.125 AC: 604 AN: 4818

European-Finnish (FIN) AF: 0.164 AC: 1739 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7573 AN: 68006

Other (OTH) AF: 0.102 AC: 216 AN: 2110

Alfa AF: 0.0337 Hom.: 27

Bravo AF: 0.102

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.47
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs13265179; hg19: chr8-9194694;