chr3-139542776-C-T

Position:

• chr3-139542776-C-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.355-35016C>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 0.0985 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 NR_121609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.02

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=-0.97).
• 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/exons	MANE	Protein	UniProt
COPB2-DT	NR_121609.1	n.355-35016C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COPB2-DT	ENST00000658348.1	n.672-35016C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0690

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0729

Gnomad4 SAS AF: 0.0752

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0785

Alfa AF: 0.108 Hom.: 434

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12493507; hg19: chr3-139261618;