3-139540884-A-T

Position:

• chr3-139540884-A-T

Variant summary

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

The NR_121609.1(COPB2-DT):​n.355-36908A>T 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 0.445 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 NR_121609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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=-0.81).
• 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/exons	MANE	UniProt
COPB2-DT	NR_121609.1	n.355-36908A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COPB2-DT	ENST00000658348.1	n.672-36908A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.485

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs190910; hg19: chr3-139259726;