rs12061474

chr1-204420186-C-T

Variant summary

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

The ENST00000443515.1(PPP1R15B-AS1):n.147-15151C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,076 control chromosomes in the GnomAD database, including 2,116 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 0.15 (2116 hom., cov: 31)
• Consequence: PPP1R15B-AS1 ENST00000443515.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

Genes affected

PPP1R15B-AS1 (HGNC:55838): (PPP1R15B and PIK3C2B antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R15B-AS1	ENST00000443515.1	n.147-15151C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22891 AN: 151958 Hom.: 2101 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0802

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.151 AC: 22937 AN: 152076 Hom.: 2116 Cov.: 31 AF XY: 0.151 AC XY: 11201 AN XY: 74362

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0804

Gnomad4 SAS AF: 0.0578

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.115

Alfa AF: 0.111 Hom.: 1502

Bravo AF: 0.149

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.9
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12061474; hg19: chr1-204389314;