chr13-46107630-C-G

Variant names:

• chr13-46107630-C-G
• rs34813434
• ENST00000415033.4:n.686-5554C>G

Variant summary

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

The ENST00000415033.4(CPB2-AS1):​n.686-5554C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,732 control chromosomes in the GnomAD database, including 23,809 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 0.55 (23809 hom., cov: 31)
• Consequence: CPB2-AS1 ENST00000415033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415033.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPB2-AS1	ENST00000415033.4	TSL:3	n.686-5554C>G		intron	N/A
	CPB2-AS1	ENST00000624622.2	TSL:6	n.980-5554C>G		intron	N/A
	CPB2-AS1	ENST00000653655.1		n.310-5554C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83279 AN: 151614 Hom.: 23795 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.549 AC: 83339 AN: 151732 Hom.: 23809 Cov.: 31 AF XY: 0.544 AC XY: 40329 AN XY: 74148

African (AFR) AF: 0.490 AC: 20246 AN: 41280

American (AMR) AF: 0.475 AC: 7242 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2008 AN: 3460

East Asian (EAS) AF: 0.190 AC: 976 AN: 5150

South Asian (SAS) AF: 0.324 AC: 1557 AN: 4808

European-Finnish (FIN) AF: 0.689 AC: 7252 AN: 10532

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42285 AN: 67944

Other (OTH) AF: 0.508 AC: 1067 AN: 2100

Alfa AF: 0.530 Hom.: 1824

Bravo AF: 0.525

Asia WGS AF: 0.321 AC: 1115 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.41
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs34813434; hg19: chr13-46681765;