13-46105463-T-C

Variant names:

• chr13-46105463-T-C
• rs2146881
• ENST00000663015.1:n.891T>C

Variant summary

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

The ENST00000663015.1(CPB2-AS1):​n.891T>C variant causes a non coding transcript exon 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 ENST00000663015.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 32 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPB2-AS1	ENST00000663015.1	n.891T>C		non_coding_transcript_exon_variant	Exon 3 of 3
CPB2-AS1	ENST00000415033.4	n.685+6682T>C		intron_variant	Intron 3 of 3	3
CPB2-AS1	ENST00000624622.2	n.979+6653T>C		intron_variant	Intron 4 of 5	6

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

African (AFR) AF: 0.762 AC: 31607 AN: 41496

American (AMR) AF: 0.776 AC: 11868 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2425 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4201 AN: 5160

South Asian (SAS) AF: 0.720 AC: 3470 AN: 4820

European-Finnish (FIN) AF: 0.832 AC: 8800 AN: 10580

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50965 AN: 67990

Other (OTH) AF: 0.733 AC: 1550 AN: 2116

Alfa AF: 0.749 Hom.: 162114

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
PhyloP100		-1.8
PromoterAI		0.0093	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2146881; hg19: chr13-46679598;