3-139540884-A-T

Variant names:

• chr3-139540884-A-T
• rs190910
• ENST00000381790.3:n.309+660A>T

Variant summary

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

The ENST00000381790.3(COPB2-DT):​n.309+660A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,074 control chromosomes in the GnomAD database, including 17,470 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 0.45 (17470 hom., cov: 33)
• Consequence: COPB2-DT ENST00000381790.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 7 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COPB2-DT	NR_121609.1	n.355-36908A>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COPB2-DT	ENST00000381790.3	n.309+660A>T		intron_variant	Intron 1 of 2	4
COPB2-DT	ENST00000515247.5	n.318-36908A>T		intron_variant	Intron 3 of 4	4
COPB2-DT	ENST00000655667.1	n.596-36908A>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67664 AN: 151956 Hom.: 17469 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.445 AC: 67673 AN: 152074 Hom.: 17470 Cov.: 33 AF XY: 0.443 AC XY: 32933 AN XY: 74340

African (AFR) AF: 0.177 AC: 7353 AN: 41480

American (AMR) AF: 0.378 AC: 5780 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2199 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1919 AN: 5172

South Asian (SAS) AF: 0.561 AC: 2702 AN: 4820

European-Finnish (FIN) AF: 0.561 AC: 5929 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39879 AN: 67966

Other (OTH) AF: 0.485 AC: 1025 AN: 2114

Alfa AF: 0.491 Hom.: 2460

Bravo AF: 0.414

Asia WGS AF: 0.443 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.52
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs190910; hg19: chr3-139259726;