rs6449093

chr4-14960872-A-G

Variant summary

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

The NR_038857.1(CPEB2-DT):n.822+24349T>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 0.16 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 NR_038857.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

Genes affected

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

LOC105374498 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CPEB2-DT	NR_038857.1	n.822+24349T>C		intron_variant, non_coding_transcript_variant
LOC105374498	XR_001741391.1	n.186+3625T>C		intron_variant, non_coding_transcript_variant
LOC105374498	XR_001741390.1	n.481+3625T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPEB2-DT	ENST00000500394.6	n.822+24349T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.0898

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0936

Gnomad4 OTH AF: 0.139

Alfa AF: 0.109 Hom.: 1672

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6449093; hg19: chr4-14962496;