rs176990

Variant names:

• chr3-139540945-T-G
• rs176990
• ENST00000381790.3:n.309+721T>G

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+721T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,070 control chromosomes in the GnomAD database, including 17,410 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 0.44 (17410 hom., cov: 32)
• Consequence: COPB2-DT ENST00000381790.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 9 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000381790.3. 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_121609.1		n.355-36847T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COPB2-DT	ENST00000381790.3	TSL:4	n.309+721T>G		intron	N/A
	COPB2-DT	ENST00000515247.5	TSL:4	n.318-36847T>G		intron	N/A
	COPB2-DT	ENST00000655667.1		n.596-36847T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67303 AN: 151952 Hom.: 17409 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.560

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: 0.443 AC: 67312 AN: 152070 Hom.: 17410 Cov.: 32 AF XY: 0.441 AC XY: 32757 AN XY: 74316

African (AFR) AF: 0.170 AC: 7043 AN: 41514

American (AMR) AF: 0.378 AC: 5774 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2203 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1914 AN: 5158

South Asian (SAS) AF: 0.559 AC: 2690 AN: 4808

European-Finnish (FIN) AF: 0.560 AC: 5911 AN: 10550

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

European-Non Finnish (NFE) AF: 0.587 AC: 39866 AN: 67956

Other (OTH) AF: 0.484 AC: 1024 AN: 2114

Alfa AF: 0.538 Hom.: 26822

Bravo AF: 0.412

Asia WGS AF: 0.442 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.5
DANN	Benign	0.73
PhyloP100		0.47

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: rs176990;

hg19: chr3-139259787;