rs11551105

chr13-110639275-G-Achr13-110639275-G-T

Variant summary

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

The NM_001242882.2(NAXD):c.*747G>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 0.111 in 155,342 control chromosomes in the GnomAD database, including 1,082 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 0.11 (1073 hom., cov: 33)
  • Exomes 𝑓: 0.057 (9 hom.)
• Consequence: NAXD NM_001242882.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAXD	NM_001242882.2	c.*747G>A		3_prime_UTR_variant	10/10	ENST00000680254.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAXD	ENST00000680254.1	c.*747G>A		3_prime_UTR_variant	10/10		NM_001242882.2	P2

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17097 AN: 152038 Hom.: 1073 Cov.: 33

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0580

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.0568 AC: 181 AN: 3186 Hom.: 9 Cov.: 0 AF XY: 0.0582 AC XY: 99 AN XY: 1700

Gnomad4 AFR exome AF: 0.0417

Gnomad4 AMR exome AF: 0.0361

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0147

Gnomad4 SAS exome AF: 0.0243

Gnomad4 FIN exome AF: 0.0769

Gnomad4 NFE exome AF: 0.0707

Gnomad4 OTH exome AF: 0.0357

GnomAD4 genome AF: 0.112 AC: 17090 AN: 152156 Hom.: 1073 Cov.: 33 AF XY: 0.114 AC XY: 8441 AN XY: 74370

Gnomad4 AFR AF: 0.0611

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0583

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0929 Hom.: 168

Bravo AF: 0.105

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.0
Dann	Benign	0.60

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: rs11551105; hg19: chr13-111291622; COSMIC: COSV57284935; COSMIC: COSV57284935;