rs4841132

Variant names:

• chr8-9326086-A-G
• rs4841132
• ENST00000520255.6:n.522A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-9326086-A-G
• chr8-9326086-A-T

Variant summary

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

The ENST00000520390.1(PPP1R3B-DT):​n.548A>G 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 0.894 in 152,496 control chromosomes in the GnomAD database, including 61,117 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 0.89 (61030 hom., cov: 34)
  • Exomes 𝑓: 0.95 (87 hom.)
• Consequence: PPP1R3B-DT ENST00000520390.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 102 publications found

Genes affected

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

LOC157273 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520390.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC157273	NR_040039.1		n.548A>G		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R3B-DT	ENST00000520255.6	TSL:3	n.522A>G		non_coding_transcript_exon	Exon 2 of 4
	PPP1R3B-DT	ENST00000520390.1	TSL:2	n.548A>G		non_coding_transcript_exon	Exon 2 of 3
	PPP1R3B-DT	ENST00000523246.2	TSL:5	n.784A>G		non_coding_transcript_exon	Exon 3 of 6

Frequencies

GnomAD3 genomes AF: 0.894 AC: 136085 AN: 152186 Hom.: 60999 Cov.: 34

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.893

GnomAD4 exome AF: 0.948 AC: 182 AN: 192 Hom.: 87 Cov.: 0 AF XY: 0.954 AC XY: 124 AN XY: 130

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 6 AN: 6

East Asian (EAS) AF: 1.00 AC: 18 AN: 18

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.958 AC: 23 AN: 24

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.939 AC: 124 AN: 132

Other (OTH) AF: 0.875 AC: 7 AN: 8

GnomAD4 genome AF: 0.894 AC: 136174 AN: 152304 Hom.: 61030 Cov.: 34 AF XY: 0.890 AC XY: 66288 AN XY: 74468

African (AFR) AF: 0.882 AC: 36648 AN: 41574

American (AMR) AF: 0.836 AC: 12792 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3274 AN: 3470

East Asian (EAS) AF: 0.988 AC: 5097 AN: 5160

South Asian (SAS) AF: 0.892 AC: 4308 AN: 4830

European-Finnish (FIN) AF: 0.838 AC: 8888 AN: 10606

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62107 AN: 68040

Other (OTH) AF: 0.888 AC: 1879 AN: 2116

Alfa AF: 0.910 Hom.: 193197

Bravo AF: 0.891

Asia WGS AF: 0.925 AC: 3218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.69
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4841132; hg19: chr8-9183596;