rs1494950

Variant names:

• chr4-14965545-A-G
• rs1494950
• ENST00000500394.6:n.822+19676T>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+19676T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,204 control chromosomes in the GnomAD database, including 1,487 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 0.097 (1487 hom., cov: 33)
• Consequence: CPEB2-DT ENST00000500394.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500394.6. 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
	CPEB2-DT	NR_038857.1		n.822+19676T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB2-DT	ENST00000500394.6	TSL:1	n.822+19676T>C		intron	N/A
	CPEB2-DT	ENST00000825730.1		n.402+27167T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0970 AC: 14754 AN: 152086 Hom.: 1485 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0260

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0193

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0971 AC: 14778 AN: 152204 Hom.: 1487 Cov.: 33 AF XY: 0.0982 AC XY: 7310 AN XY: 74420

African (AFR) AF: 0.243 AC: 10065 AN: 41480

American (AMR) AF: 0.0866 AC: 1325 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3470

East Asian (EAS) AF: 0.131 AC: 679 AN: 5176

South Asian (SAS) AF: 0.186 AC: 896 AN: 4822

European-Finnish (FIN) AF: 0.0260 AC: 276 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0193 AC: 1312 AN: 68022

Other (OTH) AF: 0.0865 AC: 183 AN: 2116

Alfa AF: 0.0689 Hom.: 123

Bravo AF: 0.106

Asia WGS AF: 0.169 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.5
DANN	Benign	0.76
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1494950;

hg19: chr4-14967169;