rs35814191

Variant names:

• chr13-46107375-TC-T
• rs35814191
• ENST00000415033.3:n.682-5808delC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000415033.3(CPB2-AS1):​n.682-5808delC 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 ENST00000415033.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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	ENST00000415033.3	n.682-5808delC		intron_variant	Intron 3 of 3	3
CPB2-AS1	ENST00000624622.2	n.980-5808delC		intron_variant	Intron 4 of 5	6
CPB2-AS1	ENST00000653655.1	n.310-5808delC		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.339

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 v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35814191; hg19: chr13-46681510;