rs2099259

chr15-82654937-C-T

Variant summary

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

The NR_046096.1(CPEB1-AS1):n.1328+4791C>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 0.462 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 NR_046096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPEB1-AS1	NR_046096.1	n.1328+4791C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPEB1-AS1	ENST00000560650.1	n.1328+4791C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.487

Alfa AF: 0.530 Hom.: 11921

Bravo AF: 0.461

Asia WGS AF: 0.507 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.47
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2099259; hg19: chr15-83323688;