rs11631963

chr15-82649451-T-C

Variant summary

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

The NR_046096.1(CPEB1-AS1):n.1040-320T>C 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 0.552 in 151,914 control chromosomes in the GnomAD database, including 23,627 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 (23627 hom., cov: 31)
• Consequence: CPEB1-AS1 NR_046096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

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 = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPEB1-AS1	NR_046096.1	n.1040-320T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPEB1-AS1	ENST00000560650.1	n.1040-320T>C		intron_variant, non_coding_transcript_variant		1
CPEB1-AS1	ENST00000654760.1	n.45-320T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83864 AN: 151796 Hom.: 23604 Cov.: 31

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.552 AC: 83927 AN: 151914 Hom.: 23627 Cov.: 31 AF XY: 0.551 AC XY: 40875 AN XY: 74244

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.561

Alfa AF: 0.605 Hom.: 29663

Bravo AF: 0.555

Asia WGS AF: 0.558 AC: 1940 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	3.0
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11631963; hg19: chr15-83318202;