rs10790286

Variant names:

• chr11-119183779-C-T
• rs10790286
• NM_001282144.2:c.*340C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024618.4(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_024618.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 29 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024618.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLRX1	NM_001282144.2	MANE Select	c.*340C>T		3_prime_UTR	Exon 10 of 10	NP_001269073.1
	NLRX1	NM_001282143.2		c.*340C>T		3_prime_UTR	Exon 10 of 10	NP_001269072.1
	NLRX1	NM_001282358.2		c.*340C>T		3_prime_UTR	Exon 10 of 10	NP_001269287.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLRX1	ENST00000409109.6	TSL:1 MANE Select	c.*340C>T		3_prime_UTR	Exon 10 of 10	ENSP00000387334.1
	NLRX1	ENST00000292199.6	TSL:1	c.*340C>T		3_prime_UTR	Exon 10 of 10	ENSP00000292199.2
	NLRX1	ENST00000409991.5	TSL:1	c.*340C>T		3_prime_UTR	Exon 10 of 10	ENSP00000386851.1

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

GnomAD2 exomes AF: 0.454 AC: 112666 AN: 248224 AF XY: 0.456

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 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

African (AFR) AF: 0.565 AC: 9994 AN: 17688

American (AMR) AF: 0.309 AC: 13485 AN: 43656

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 11062 AN: 20978

East Asian (EAS) AF: 0.666 AC: 23993 AN: 36046

South Asian (SAS) AF: 0.445 AC: 31001 AN: 69742

European-Finnish (FIN) AF: 0.499 AC: 26399 AN: 52888

Middle Eastern (MID) AF: 0.477 AC: 1977 AN: 4146

European-Non Finnish (NFE) AF: 0.436 AC: 152597 AN: 349740

Other (OTH) AF: 0.466 AC: 15406 AN: 33062

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

African (AFR) AF: 0.555 AC: 23008 AN: 41450

American (AMR) AF: 0.373 AC: 5697 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1815 AN: 3468

East Asian (EAS) AF: 0.665 AC: 3428 AN: 5152

South Asian (SAS) AF: 0.446 AC: 2152 AN: 4820

European-Finnish (FIN) AF: 0.517 AC: 5460 AN: 10562

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29545 AN: 67968

Other (OTH) AF: 0.466 AC: 981 AN: 2104

Alfa AF: 0.451 Hom.: 18406

Bravo AF: 0.476

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10790286; hg19: chr11-119054488; COSMIC: COSV52702598; COSMIC: COSV52702598;