13-46105463-T-C

Position:

• chr13-46105463-T-C

Variant summary

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

The ENST00000663159.1(CPB2-AS1):​n.470-46031T>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 0.76 in 152,122 control chromosomes in the GnomAD database, including 44,156 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 0.76 (44156 hom., cov: 32)
• Consequence: CPB2-AS1 ENST00000663159.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

CPB2-AS1 (HGNC:39898): (CPB2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPB2-AS1	ENST00000663159.1	n.470-46031T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115584 AN: 152004 Hom.: 44110 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.760 AC: 115688 AN: 152122 Hom.: 44156 Cov.: 32 AF XY: 0.764 AC XY: 56809 AN XY: 74378

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.733

Alfa AF: 0.744 Hom.: 70496

Bravo AF: 0.756

Asia WGS AF: 0.772 AC: 2681 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2146881; hg19: chr13-46679598;