rs11551105

Variant names:

• chr13-110639275-G-A
• rs11551105
• NM_001242882.2:c.*747G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-110639275-G-A
• chr13-110639275-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

NAXD Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• NAD(P)HX dehydratase deficiency

  Inheritance: AR, AD Classification: DEFINITIVE, MODERATE Submitted by: Baylor College of Medicine Research Center, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242882.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAXD	NM_001242882.2	MANE Select	c.*747G>A		3_prime_UTR	Exon 10 of 10	NP_001229811.1
	NAXD	NM_018210.4		c.*754G>A		3_prime_UTR	Exon 10 of 10	NP_060680.2
	NAXD	NM_001242881.2		c.*747G>A		3_prime_UTR	Exon 10 of 10	NP_001229810.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAXD	ENST00000680254.1	MANE Select	c.*747G>A		3_prime_UTR	Exon 10 of 10	ENSP00000505619.1
	NAXD	ENST00000309957.3	TSL:2	c.*754G>A		3_prime_UTR	Exon 10 of 10	ENSP00000311984.2
	NAXD	ENST00000957157.1		c.*747G>A		3_prime_UTR	Exon 11 of 11	ENSP00000627216.1

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

African (AFR) AF: 0.0417 AC: 1 AN: 24

American (AMR) AF: 0.0361 AC: 23 AN: 638

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20

East Asian (EAS) AF: 0.0147 AC: 1 AN: 68

South Asian (SAS) AF: 0.0243 AC: 7 AN: 288

European-Finnish (FIN) AF: 0.0769 AC: 2 AN: 26

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0707 AC: 144 AN: 2038

Other (OTH) AF: 0.0357 AC: 3 AN: 84

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

African (AFR) AF: 0.0611 AC: 2536 AN: 41534

American (AMR) AF: 0.104 AC: 1592 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3468

East Asian (EAS) AF: 0.103 AC: 534 AN: 5170

South Asian (SAS) AF: 0.0583 AC: 281 AN: 4820

European-Finnish (FIN) AF: 0.198 AC: 2096 AN: 10578

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9125 AN: 67998

Other (OTH) AF: 0.125 AC: 264 AN: 2112

Alfa AF: 0.0917 Hom.: 168

Bravo AF: 0.105

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-0.95
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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