chr11-119173368-C-T

Position:

• chr11-119173368-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001282144.2(NLRX1):​c.230-111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00137 in 1,194,874 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency:
  • Genomes: 𝑓 0.00091 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0014 (1 hom.)
• Consequence: NLRX1 NM_001282144.2 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -0.0110

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NLRX1	NM_001282144.2	c.230-111C>T		intron_variant		ENST00000409109.6	NP_001269073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NLRX1	ENST00000409109.6	c.230-111C>T		intron_variant		1	NM_001282144.2	ENSP00000387334	P1

Frequencies

GnomAD3 genomes AF: 0.000914 AC: 139 AN: 152098 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00147

Gnomad OTH AF: 0.00239

GnomAD4 exome AF: 0.00144 AC: 1504 AN: 1042658 Hom.: 1 Cov.: 14 AF XY: 0.00140 AC XY: 735 AN XY: 524772

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000291

Gnomad4 ASJ exome AF: 0.000218

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000819

Gnomad4 FIN exome AF: 0.00210

Gnomad4 NFE exome AF: 0.00165

Gnomad4 OTH exome AF: 0.00159

GnomAD4 genome AF: 0.000907 AC: 138 AN: 152216 Hom.: 0 Cov.: 32 AF XY: 0.000928 AC XY: 69 AN XY: 74392

Gnomad4 AFR AF: 0.000193

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00186

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00147

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.000318 Hom.: 0

Bravo AF: 0.000869

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

literature only

Human Evolutionary Genetics, Institut Pasteur

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.77

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: rs199476038; hg19: chr11-119044077;