rs2099259

Variant names:

• chr15-82654937-C-T
• rs2099259
• ENST00000560650.1:n.1328+4791C>T

Variant summary

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

The ENST00000560650.1(CPEB1-AS1):​n.1328+4791C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,146 control chromosomes in the GnomAD database, including 17,145 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 0.46 (17145 hom., cov: 33)
• Consequence: CPEB1-AS1 ENST00000560650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 8 publications found

Genes affected

CPEB1-AS1 (HGNC:27523): (CPEB1 antisense RNA 1)

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 (NFE) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560650.1. 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
	CPEB1-AS1	NR_046096.1		n.1328+4791C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB1-AS1	ENST00000560650.1	TSL:1	n.1328+4791C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70190 AN: 152028 Hom.: 17132 Cov.: 33

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.462 AC: 70224 AN: 152146 Hom.: 17145 Cov.: 33 AF XY: 0.460 AC XY: 34183 AN XY: 74376

African (AFR) AF: 0.285 AC: 11825 AN: 41500

American (AMR) AF: 0.509 AC: 7784 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3468

East Asian (EAS) AF: 0.534 AC: 2764 AN: 5174

South Asian (SAS) AF: 0.494 AC: 2387 AN: 4830

European-Finnish (FIN) AF: 0.444 AC: 4690 AN: 10566

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37307 AN: 68012

Other (OTH) AF: 0.487 AC: 1023 AN: 2102

Alfa AF: 0.529 Hom.: 13100

Bravo AF: 0.461

Asia WGS AF: 0.507 AC: 1761 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	0.47
DANN	Benign	0.67
PhyloP100		-1.0

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: rs2099259;

hg19: chr15-83323688;