rs12493507

Variant names:

• chr3-139542776-C-T
• rs12493507
• ENST00000381790.3:n.309+2552C>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+2552C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0985 in 152,150 control chromosomes in the GnomAD database, including 793 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 0.098 (793 hom., cov: 33)
• Consequence: COPB2-DT ENST00000381790.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.02
• Publications: 8 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COPB2-DT	NR_121609.1	n.355-35016C>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+2552C>T		intron_variant	Intron 1 of 2	4
COPB2-DT	ENST00000515247.5	n.318-35016C>T		intron_variant	Intron 3 of 4	4
COPB2-DT	ENST00000655667.1	n.596-35016C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14962 AN: 152032 Hom.: 793 Cov.: 33

Gnomad AFR AF: 0.0689

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0985 AC: 14983 AN: 152150 Hom.: 793 Cov.: 33 AF XY: 0.100 AC XY: 7445 AN XY: 74360

African (AFR) AF: 0.0690 AC: 2864 AN: 41514

American (AMR) AF: 0.123 AC: 1887 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3470

East Asian (EAS) AF: 0.0729 AC: 376 AN: 5156

South Asian (SAS) AF: 0.0752 AC: 362 AN: 4812

European-Finnish (FIN) AF: 0.135 AC: 1433 AN: 10586

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7679 AN: 68012

Other (OTH) AF: 0.0785 AC: 166 AN: 2114

Alfa AF: 0.108 Hom.: 475

Bravo AF: 0.0975

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.011
DANN	Benign	0.40
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs12493507; hg19: chr3-139261618;