rs176990

chr3-139540945-T-G

Variant summary

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

The NR_121609.1(COPB2-DT):n.355-36847T>G variant causes a intron, non coding transcript 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 NR_121609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

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=-0.8).
• 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/exons	MANE	UniProt
COPB2-DT	NR_121609.1	n.355-36847T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COPB2-DT	ENST00000658348.1	n.672-36847T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.484

Alfa AF: 0.542 Hom.: 23010

Bravo AF: 0.412

Asia WGS AF: 0.442 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	7.5
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs176990; hg19: chr3-139259787;