rs6449093

Variant names:

• chr4-14960872-A-G
• rs6449093
• ENST00000500394.6:n.822+24349T>C

Variant summary

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

The ENST00000500394.6(CPEB2-DT):​n.822+24349T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,052 control chromosomes in the GnomAD database, including 2,659 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 0.16 (2659 hom., cov: 31)
• Consequence: CPEB2-DT ENST00000500394.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 5 publications found

Genes affected

CPEB2-DT (HGNC:49082): (CPEB2 divergent transcript)

LOC105374498 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPEB2-DT	NR_038857.1	n.822+24349T>C		intron_variant	Intron 7 of 7
LOC105374498	XR_001741390.1	n.481+3625T>C		intron_variant	Intron 2 of 2
LOC105374498	XR_001741391.1	n.186+3625T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPEB2-DT	ENST00000500394.6	n.822+24349T>C		intron_variant	Intron 7 of 7	1
CPEB2-DT	ENST00000825730.1	n.403-22566T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24345 AN: 151936 Hom.: 2655 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.160 AC: 24375 AN: 152052 Hom.: 2659 Cov.: 31 AF XY: 0.163 AC XY: 12100 AN XY: 74318

African (AFR) AF: 0.305 AC: 12635 AN: 41420

American (AMR) AF: 0.0898 AC: 1374 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3468

East Asian (EAS) AF: 0.130 AC: 673 AN: 5168

South Asian (SAS) AF: 0.256 AC: 1231 AN: 4814

European-Finnish (FIN) AF: 0.128 AC: 1359 AN: 10590

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0936 AC: 6365 AN: 67978

Other (OTH) AF: 0.139 AC: 293 AN: 2108

Alfa AF: 0.111 Hom.: 2457

Bravo AF: 0.158

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.74
DANN	Benign	0.68
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6449093; hg19: chr4-14962496;