rs72823592

Positions:

• chr17-48045642-G-A
• chr17-48045642-G-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+1567C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,298 control chromosomes in the GnomAD database, including 2,959 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 0.18 (2955 hom., cov: 32)
  • Exomes 𝑓: 0.22 (4 hom.)
• Consequence: COPZ2 XM_047436209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.08

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COPZ2	XM_047436209.1	c.-25+1567C>T		intron_variant			XP_047292165.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFE2L1-DT	ENST00000578660.2	n.2466C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27038 AN: 152060 Hom.: 2956 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.217 AC: 26 AN: 120 Hom.: 4 Cov.: 0 AF XY: 0.176 AC XY: 18 AN XY: 102

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.256

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.178 AC: 27037 AN: 152178 Hom.: 2955 Cov.: 32 AF XY: 0.175 AC XY: 13023 AN XY: 74382

Gnomad4 AFR AF: 0.0998

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.161

Alfa AF: 0.168 Hom.: 591

Bravo AF: 0.163

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.011
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72823592; hg19: chr17-46123004;