rs3102078

Variant names:

• chr8-9193215-C-A
• rs3102078
• ENST00000512942.9:n.300+3618C>A

Variant summary

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

The ENST00000512942.9(PPP1R3B-DT):​n.300+3618C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,920 control chromosomes in the GnomAD database, including 26,486 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 0.58 (26486 hom., cov: 31)
• Consequence: PPP1R3B-DT ENST00000512942.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 4 publications found

Genes affected

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

LOC101929128 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929128	NR_125431.1	n.287+3629C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000512942.9	n.300+3618C>A		intron_variant	Intron 2 of 3	1
PPP1R3B-DT	ENST00000417333.8	n.647+3629C>A		intron_variant	Intron 4 of 5	5
PPP1R3B-DT	ENST00000523747.1	n.83-743C>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88770 AN: 151802 Hom.: 26474 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.585 AC: 88818 AN: 151920 Hom.: 26486 Cov.: 31 AF XY: 0.572 AC XY: 42503 AN XY: 74246

African (AFR) AF: 0.578 AC: 23933 AN: 41390

American (AMR) AF: 0.592 AC: 9037 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2639 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1476 AN: 5144

South Asian (SAS) AF: 0.403 AC: 1946 AN: 4824

European-Finnish (FIN) AF: 0.462 AC: 4871 AN: 10546

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42805 AN: 67968

Other (OTH) AF: 0.617 AC: 1298 AN: 2104

Alfa AF: 0.607 Hom.: 3902

Bravo AF: 0.596

Asia WGS AF: 0.361 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.054
DANN	Benign	0.61
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs3102078; hg19: chr8-9050725;