rs16849065

Variant names:

• chr3-139442510-A-G
• rs16849065
• ENST00000504670.7:n.542-1784A>G

Variant summary

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

The ENST00000504670.7(COPB2-DT):​n.542-1784A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,068 control chromosomes in the GnomAD database, including 1,780 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 0.11 (1780 hom., cov: 32)
• Consequence: COPB2-DT ENST00000504670.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

COPB2-DT (HGNC:55579): (COPB2 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COPB2-DT	NR_121608.1	n.355-1784A>G		intron_variant	Intron 3 of 3
COPB2-DT	NR_121609.1	n.354+19396A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COPB2-DT	ENST00000504670.7	n.542-1784A>G		intron_variant	Intron 2 of 2	2
COPB2-DT	ENST00000507362.5	n.520-1784A>G		intron_variant	Intron 2 of 2	4
COPB2-DT	ENST00000510068.5	n.196-7770A>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16628 AN: 151950 Hom.: 1774 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.0292

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0255

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0403

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.110 AC: 16657 AN: 152068 Hom.: 1780 Cov.: 32 AF XY: 0.107 AC XY: 7951 AN XY: 74356

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.0847

Gnomad4 EAS AF: 0.0291

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.0255

Gnomad4 NFE AF: 0.0403

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0789 Hom.: 162

Bravo AF: 0.119

Asia WGS AF: 0.0910 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16849065; hg19: chr3-139161352;