chr3-139442510-A-G

Variant names:

• chr3-139442510-A-G
• rs16849065
• ENST00000504670.8:n.542-1784A>G

Variant summary

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

The ENST00000504670.8(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 ENST00000504670.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504670.8. 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
	COPB2-DT	NR_121608.1		n.355-1784A>G		intron	N/A
	COPB2-DT	NR_121609.1		n.354+19396A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COPB2-DT	ENST00000504670.8	TSL:2	n.542-1784A>G		intron	N/A
	COPB2-DT	ENST00000507362.6	TSL:4	n.532-1784A>G		intron	N/A
	COPB2-DT	ENST00000510068.5	TSL:3	n.196-7770A>G		intron	N/A

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

African (AFR) AF: 0.276 AC: 11446 AN: 41406

American (AMR) AF: 0.0659 AC: 1008 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0847 AC: 294 AN: 3472

East Asian (EAS) AF: 0.0291 AC: 150 AN: 5160

South Asian (SAS) AF: 0.0972 AC: 468 AN: 4814

European-Finnish (FIN) AF: 0.0255 AC: 270 AN: 10606

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0403 AC: 2740 AN: 68004

Other (OTH) AF: 0.100 AC: 211 AN: 2110

Alfa AF: 0.0863 Hom.: 205

Bravo AF: 0.119

Asia WGS AF: 0.0910 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.63
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16849065;

hg19: chr3-139161352;