rs11631963

Variant names:

• chr15-82649451-T-C
• rs11631963
• ENST00000560650.1:n.1040-320T>C

Variant summary

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

The ENST00000560650.1(CPEB1-AS1):​n.1040-320T>C variant causes a intron 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 ENST00000560650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 5 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 = 0.611 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.1040-320T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB1-AS1	ENST00000560650.1	TSL:1	n.1040-320T>C		intron	N/A
	CPEB1-AS1	ENST00000654760.2		n.705-320T>C		intron	N/A

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

African (AFR) AF: 0.429 AC: 17762 AN: 41406

American (AMR) AF: 0.596 AC: 9102 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3470

East Asian (EAS) AF: 0.554 AC: 2854 AN: 5152

South Asian (SAS) AF: 0.522 AC: 2509 AN: 4806

European-Finnish (FIN) AF: 0.568 AC: 5992 AN: 10542

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41834 AN: 67956

Other (OTH) AF: 0.561 AC: 1179 AN: 2100

Alfa AF: 0.587 Hom.: 50563

Bravo AF: 0.555

Asia WGS AF: 0.558 AC: 1940 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	3.0
DANN	Benign	0.62
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs11631963; hg19: chr15-83318202;