15-82654567-A-G

Position:

• chr15-82654567-A-G

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+4421A>G 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 0.551 in 151,990 control chromosomes in the GnomAD database, including 23,559 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 0.55 (23559 hom., cov: 31)
• Consequence: CPEB1-AS1 NR_046096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPEB1-AS1	NR_046096.1	n.1328+4421A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPEB1-AS1	ENST00000560650.1	n.1328+4421A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83753 AN: 151872 Hom.: 23534 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.551 AC: 83818 AN: 151990 Hom.: 23559 Cov.: 31 AF XY: 0.549 AC XY: 40802 AN XY: 74284

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.561

Alfa AF: 0.512 Hom.: 2049

Bravo AF: 0.554

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1864699; hg19: chr15-83323318;