rs330564

Positions:

• chr13-110638697-T-C
• chr13-110638697-T-G

Variant summary

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

The NM_001242882.2(NAXD):​c.*169T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 798,342 control chromosomes in the GnomAD database, including 35,964 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 0.31 (7772 hom., cov: 33)
  • Exomes 𝑓: 0.28 (28192 hom.)
• Consequence: NAXD NM_001242882.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAXD	NM_001242882.2	c.*169T>C		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.*169T>C		3_prime_UTR_variant	10/10		NM_001242882.2	ENSP00000505619	P2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47781 AN: 151940 Hom.: 7752 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.307

GnomAD3 exomes AF: 0.339 AC: 45407 AN: 133850 Hom.: 8471 AF XY: 0.329 AC XY: 24066 AN XY: 73156

Gnomad AFR exome AF: 0.365

Gnomad AMR exome AF: 0.535

Gnomad ASJ exome AF: 0.308

Gnomad EAS exome AF: 0.308

Gnomad SAS exome AF: 0.319

Gnomad FIN exome AF: 0.310

Gnomad NFE exome AF: 0.269

Gnomad OTH exome AF: 0.316

GnomAD4 exome AF: 0.285 AC: 183949 AN: 646284 Hom.: 28192 Cov.: 8 AF XY: 0.284 AC XY: 97995 AN XY: 344450

Gnomad4 AFR exome AF: 0.353

Gnomad4 AMR exome AF: 0.517

Gnomad4 ASJ exome AF: 0.299

Gnomad4 EAS exome AF: 0.306

Gnomad4 SAS exome AF: 0.318

Gnomad4 FIN exome AF: 0.315

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.295

GnomAD4 genome AF: 0.315 AC: 47843 AN: 152058 Hom.: 7772 Cov.: 33 AF XY: 0.319 AC XY: 23727 AN XY: 74318

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.307

Alfa AF: 0.290 Hom.: 6960

Bravo AF: 0.329

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.41

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: rs330564; hg19: chr13-111291044; COSMIC: COSV57288586; COSMIC: COSV57288586;