rs11637433

chr15-82652585-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+2439A>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 0.574 in 152,056 control chromosomes in the GnomAD database, including 25,243 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 0.57 (25242 hom., cov: 33)
  • Exomes 𝑓: 0.63 (1 hom.)
• Consequence: CPEB1-AS1 NR_046096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

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=-0.99).
• 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	UniProt
CPEB1-AS1	NR_046096.1	n.1328+2439A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPEB1-AS1	ENST00000560650.1	n.1328+2439A>G		intron_variant, non_coding_transcript_variant		1
CPEB1-AS1	ENST00000618020.1	n.2557A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87253 AN: 151930 Hom.: 25203 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.572

GnomAD4 exome AF: 0.625 AC: 5 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.574 AC: 87342 AN: 152048 Hom.: 25242 Cov.: 33 AF XY: 0.572 AC XY: 42508 AN XY: 74308

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.574

Alfa AF: 0.606 Hom.: 9593

Bravo AF: 0.581

Asia WGS AF: 0.561 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.22
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11637433; hg19: chr15-83321336;