rs35814191

Variant names:

• chr13-46107375-TC-T
• rs35814191
• ENST00000415033.4:n.686-5808delC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000415033.4(CPB2-AS1):​n.686-5808delC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (8818 hom., cov: 0)
• Consequence: CPB2-AS1 ENST00000415033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPB2-AS1	ENST00000415033.4	TSL:3	n.686-5808delC		intron	N/A
	CPB2-AS1	ENST00000624622.2	TSL:6	n.980-5808delC		intron	N/A
	CPB2-AS1	ENST00000653655.1		n.310-5808delC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51417 AN: 151906 Hom.: 8808 Cov.: 0

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.338 AC: 51459 AN: 152024 Hom.: 8818 Cov.: 0 AF XY: 0.338 AC XY: 25127 AN XY: 74318

African (AFR) AF: 0.345 AC: 14322 AN: 41462

American (AMR) AF: 0.321 AC: 4903 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3472

East Asian (EAS) AF: 0.182 AC: 944 AN: 5174

South Asian (SAS) AF: 0.223 AC: 1076 AN: 4822

European-Finnish (FIN) AF: 0.404 AC: 4272 AN: 10576

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23446 AN: 67936

Other (OTH) AF: 0.339 AC: 716 AN: 2112

Alfa AF: 0.347 Hom.: 1105

Bravo AF: 0.329

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs35814191; hg19: chr13-46681510;