rs10790286

Positions:

• chr11-119183779-C-T

Variant summary

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

The NM_001282144.2(NLRX1):​c.*340C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 779,954 control chromosomes in the GnomAD database, including 84,794 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 0.48 (17824 hom., cov: 32)
  • Exomes 𝑓: 0.46 (66970 hom.)
• Consequence: NLRX1 NM_001282144.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

NLRX1 (HGNC:29890): (NLR family member X1) The protein encoded by this gene is a member of the NLR family and localizes to the outer mitochondrial membrane. The encoded protein is a regulator of mitochondrial antivirus responses. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NLRX1	NM_001282144.2	c.*340C>T		3_prime_UTR_variant	10/10	ENST00000409109.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NLRX1	ENST00000409109.6	c.*340C>T		3_prime_UTR_variant	10/10	1	NM_001282144.2	P1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72459 AN: 151890 Hom.: 17795 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.467

GnomAD3 exomes AF: 0.454 AC: 112666 AN: 248224 Hom.: 26557 AF XY: 0.456 AC XY: 61451 AN XY: 134654

Gnomad AFR exome AF: 0.563

Gnomad AMR exome AF: 0.299

Gnomad ASJ exome AF: 0.522

Gnomad EAS exome AF: 0.672

Gnomad SAS exome AF: 0.448

Gnomad FIN exome AF: 0.503

Gnomad NFE exome AF: 0.438

Gnomad OTH exome AF: 0.443

GnomAD4 exome AF: 0.455 AC: 285914 AN: 627946 Hom.: 66970 Cov.: 0 AF XY: 0.455 AC XY: 155541 AN XY: 342076

Gnomad4 AFR exome AF: 0.565

Gnomad4 AMR exome AF: 0.309

Gnomad4 ASJ exome AF: 0.527

Gnomad4 EAS exome AF: 0.666

Gnomad4 SAS exome AF: 0.445

Gnomad4 FIN exome AF: 0.499

Gnomad4 NFE exome AF: 0.436

Gnomad4 OTH exome AF: 0.466

GnomAD4 genome AF: 0.477 AC: 72533 AN: 152008 Hom.: 17824 Cov.: 32 AF XY: 0.481 AC XY: 35725 AN XY: 74286

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.466

Alfa AF: 0.443 Hom.: 11349

Bravo AF: 0.476

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10790286; hg19: chr11-119054488; COSMIC: COSV52702598; COSMIC: COSV52702598;