rs330563

Positions:

• chr13-110638533-G-A
• chr13-110638533-G-C

Variant summary

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

The NM_001242882.2(NAXD):​c.*5G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,610,948 control chromosomes in the GnomAD database, including 70,234 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 0.35 (10127 hom., cov: 33)
  • Exomes 𝑓: 0.28 (60107 hom.)
• Consequence: NAXD NM_001242882.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

Genes affected

NAXD (HGNC:25576): (NAD(P)HX dehydratase) Enables ATP-dependent NAD(P)H-hydrate dehydratase activity. Predicted to be involved in metabolite repair. Predicted to be located in cytosol; endoplasmic reticulum; and mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAXD	NM_001242882.2	c.*5G>A		3_prime_UTR_variant	10/10	ENST00000680254.1	NP_001229811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAXD	ENST00000680254.1	c.*5G>A		3_prime_UTR_variant	10/10		NM_001242882.2	ENSP00000505619.1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52991 AN: 151944 Hom.: 10084 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.333

GnomAD3 exomes AF: 0.334 AC: 82715 AN: 247394 Hom.: 15413 AF XY: 0.322 AC XY: 43275 AN XY: 134540

Gnomad AFR exome AF: 0.491

Gnomad AMR exome AF: 0.549

Gnomad ASJ exome AF: 0.312

Gnomad EAS exome AF: 0.310

Gnomad SAS exome AF: 0.314

Gnomad FIN exome AF: 0.309

Gnomad NFE exome AF: 0.263

Gnomad OTH exome AF: 0.314

GnomAD4 exome AF: 0.280 AC: 407853 AN: 1458886 Hom.: 60107 Cov.: 34 AF XY: 0.279 AC XY: 202567 AN XY: 725462

Gnomad4 AFR exome AF: 0.495

Gnomad4 AMR exome AF: 0.533

Gnomad4 ASJ exome AF: 0.301

Gnomad4 EAS exome AF: 0.307

Gnomad4 SAS exome AF: 0.316

Gnomad4 FIN exome AF: 0.312

Gnomad4 NFE exome AF: 0.256

Gnomad4 OTH exome AF: 0.290

GnomAD4 genome AF: 0.349 AC: 53094 AN: 152062 Hom.: 10127 Cov.: 33 AF XY: 0.353 AC XY: 26205 AN XY: 74322

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.333

Alfa AF: 0.272 Hom.: 7650

Bravo AF: 0.368

Asia WGS AF: 0.310 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.43
DANN	Benign	0.74
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs330563; hg19: chr13-111290880; COSMIC: COSV57284841; COSMIC: COSV57284841;