1-204420186-C-T

Variant names:

• chr1-204420186-C-T
• rs12061474
• ENST00000443515.1:n.147-15151C>T

Variant summary

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

The ENST00000443515.1(PPP1R15B-AS1):​n.147-15151C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443515.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R15B-AS1	ENST00000443515.1	TSL:3	n.147-15151C>T		intron	N/A
	PPP1R15B-AS1	ENST00000775926.1		n.155-15151C>T		intron	N/A
	PPP1R15B-AS1	ENST00000775927.1		n.350-15151C>T		intron	N/A

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

African (AFR) AF: 0.254 AC: 10537 AN: 41438

American (AMR) AF: 0.110 AC: 1681 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3470

East Asian (EAS) AF: 0.0804 AC: 416 AN: 5176

South Asian (SAS) AF: 0.0578 AC: 279 AN: 4824

European-Finnish (FIN) AF: 0.171 AC: 1812 AN: 10578

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

European-Non Finnish (NFE) AF: 0.111 AC: 7544 AN: 67996

Other (OTH) AF: 0.115 AC: 242 AN: 2110

Alfa AF: 0.115 Hom.: 2231

Bravo AF: 0.149

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.60
PhyloP100		0.075

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12061474;

hg19: chr1-204389314;