1-156591765-G-GGGGTCGGGCC

Variant summary

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

The ENST00000368234.7(NAXE):c.-37_-36insTCGGGCCGGG 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 0.28 (6453 hom., cov: 0)
  • Exomes 𝑓: 0.26 (38205 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-GGGGTCGGGCC is Benign according to our data. Variant chr1-156591765-G-GGGGTCGGGCC is described in ClinVar as [Benign]. Clinvar id is 1247761.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 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: 0.285 AC: 42786 AN: 150244 Hom.: 6434 Cov.: 0

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.296

GnomAD3 exomes AF: 0.295 AC: 442 AN: 1496 Hom.: 92 AF XY: 0.299 AC XY: 260 AN XY: 870

Gnomad AFR exome AF: 0.156

Gnomad AMR exome AF: 0.333

Gnomad ASJ exome AF: 0.833

Gnomad EAS exome AF: 0.500

Gnomad SAS exome AF: 0.639

Gnomad FIN exome AF: 0.293

Gnomad NFE exome AF: 0.284

Gnomad OTH exome AF: 0.250

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.259 AC: 274374 AN: 1060848 Hom.: 38205 Cov.: 53 AF XY: 0.261 AC XY: 132188 AN XY: 505804

Gnomad4 AFR exome AF: 0.343

Gnomad4 AMR exome AF: 0.309

Gnomad4 ASJ exome AF: 0.330

Gnomad4 EAS exome AF: 0.498

Gnomad4 SAS exome AF: 0.515

Gnomad4 FIN exome AF: 0.266

Gnomad4 NFE exome AF: 0.241

Gnomad4 OTH exome AF: 0.293

GnomAD4 genome AF: 0.285 AC: 42841 AN: 150346 Hom.: 6453 Cov.: 0 AF XY: 0.290 AC XY: 21280 AN XY: 73442

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.303

Alfa AF: 0.168 Hom.: 184

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 10, 2021

- -

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: rs149629319; hg19: chr1-156561557;