1-156591765-G-GGGGCCGGGCCGGGCC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000368234.7(NAXE):c.-36_-22dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.050 (271 hom., cov: 0)
  • Exomes 𝑓: 0.032 (673 hom.)
  • Failed GnomAD Quality Control
• Consequence: NAXE ENST00000368234.7 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.189

Genes affected

NAXE (HGNC:18453): (NAD(P)HX epimerase) The product of this gene interacts with apolipoprotein A-I (apoA-I), the major apolipoprotein of high-density lipoproteins (HDLs). It is secreted into some bodily fluids, and its synthesis and secretion are stimulated in vitro by incubating cells with apoA-I. The human genome contains related pseudogenes. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-156591765-G-GGGGCCGGGCCGGGCC is Benign according to our data. Variant chr1-156591765-G-GGGGCCGGGCCGGGCC is described in ClinVar as [Benign]. Clinvar id is 1239516.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAXE	NM_144772.3			upstream_gene_variant		ENST00000368235.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAXE	ENST00000368235.8			upstream_gene_variant		1	NM_144772.3	P1

Frequencies

GnomAD3 genomes AF: 0.0498 AC: 7484 AN: 150208 Hom.: 269 Cov.: 0

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0183

Gnomad EAS AF: 0.0259

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0362

Gnomad OTH AF: 0.0470

GnomAD3 exomes AF: 0.0261 AC: 39 AN: 1496 Hom.: 0 AF XY: 0.0276 AC XY: 24 AN XY: 870

Gnomad AFR exome AF: 0.0313

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0115

Gnomad NFE exome AF: 0.0353

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0324 AC: 34304 AN: 1059276 Hom.: 673 Cov.: 53 AF XY: 0.0320 AC XY: 16165 AN XY: 504936

Gnomad4 AFR exome AF: 0.0832

Gnomad4 AMR exome AF: 0.0197

Gnomad4 ASJ exome AF: 0.0147

Gnomad4 EAS exome AF: 0.0163

Gnomad4 SAS exome AF: 0.0652

Gnomad4 FIN exome AF: 0.00930

Gnomad4 NFE exome AF: 0.0315

Gnomad4 OTH exome AF: 0.0333

GnomAD4 genome AF: 0.0499 AC: 7502 AN: 150310 Hom.: 271 Cov.: 0 AF XY: 0.0494 AC XY: 3630 AN XY: 73428

Gnomad4 AFR AF: 0.0870

Gnomad4 AMR AF: 0.0370

Gnomad4 ASJ AF: 0.0183

Gnomad4 EAS AF: 0.0262

Gnomad4 SAS AF: 0.0832

Gnomad4 FIN AF: 0.0106

Gnomad4 NFE AF: 0.0362

Gnomad4 OTH AF: 0.0469

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58410616; hg19: chr1-156561557;