chr3-139495628-A-T

Position:

• chr3-139495628-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.354+72514A>T variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.151 in 151,590 control chromosomes in the GnomAD database, including 3,823 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 0.15 (3823 hom., cov: 31)
• Consequence: COPB2-DT NR_121609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.73

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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COPB2-DT	NR_121609.1	n.354+72514A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COPB2-DT	ENST00000658348.1	n.671+72514A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22864 AN: 151476 Hom.: 3816 Cov.: 31

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.0859

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.151 AC: 22880 AN: 151590 Hom.: 3823 Cov.: 31 AF XY: 0.164 AC XY: 12166 AN XY: 74082

Gnomad4 AFR AF: 0.0453

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.0897

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.142

Alfa AF: 0.123 Hom.: 237

Bravo AF: 0.165

Asia WGS AF: 0.499 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2165139; hg19: chr3-139214470;