rs3764400

Positions:

• chr17-48046570-T-C

Variant summary

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

The XM_047436209.1(COPZ2):​c.-25+639A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,200 control chromosomes in the GnomAD database, including 1,560 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 0.12 (1560 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: COPZ2 XM_047436209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520

Genes affected

COPZ2 (HGNC:):

NFE2L1-DT (HGNC:54812): (NFE2L1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COPZ2	XM_047436209.1	c.-25+639A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFE2L1-DT	ENST00000578660.2	n.1538A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18097 AN: 152082 Hom.: 1559 Cov.: 32

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.0854

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.113

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.119 AC: 18104 AN: 152200 Hom.: 1560 Cov.: 32 AF XY: 0.123 AC XY: 9145 AN XY: 74412

Gnomad4 AFR AF: 0.0336

Gnomad4 AMR AF: 0.0854

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.115

Alfa AF: 0.140 Hom.: 2437

Bravo AF: 0.107

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3764400; hg19: chr17-46123932;