rs11637433

Variant names:

• chr15-82652585-A-G
• rs11637433
• ENST00000560650.1:n.1328+2439A>G

Variant summary

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

The ENST00000560650.1(CPEB1-AS1):​n.1328+2439A>G variant causes a intron 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 ENST00000560650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• 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=-0.99).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB1-AS1	NR_046096.1		n.1328+2439A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB1-AS1	ENST00000560650.1	TSL:1	n.1328+2439A>G		intron	N/A
	CPEB1-AS1	ENST00000618020.1	TSL:6	n.2557A>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.506 AC: 20996 AN: 41460

American (AMR) AF: 0.606 AC: 9269 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2112 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2779 AN: 5176

South Asian (SAS) AF: 0.520 AC: 2508 AN: 4826

European-Finnish (FIN) AF: 0.569 AC: 6003 AN: 10558

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.616 AC: 41870 AN: 67952

Other (OTH) AF: 0.574 AC: 1212 AN: 2112

Alfa AF: 0.604 Hom.: 11813

Bravo AF: 0.581

Asia WGS AF: 0.561 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.22
DANN	Benign	0.36
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11637433; hg19: chr15-83321336;