NM_031490.5:c.1939-3517C>T

Variant names:

• chr16-48343990-C-T
• rs16946122
• NM_031490.5:c.1939-3517C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031490.5(LONP2):​c.1939-3517C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 152,176 control chromosomes in the GnomAD database, including 554 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 0.082 (554 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LONP2 NM_031490.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 10 publications found

Genes affected

LONP2 (HGNC:20598): (lon peptidase 2, peroxisomal) In human, peroxisomes function primarily to catalyze fatty acid beta-oxidation and, as a by-product, produce hydrogen peroxide and superoxide. The protein encoded by this gene is an ATP-dependent protease that likely plays a role in maintaining overall peroxisome homeostasis as well as proteolytically degrading peroxisomal proteins damaged by oxidation. The protein has an N-terminal Lon N substrate recognition domain, an ATPase domain, a proteolytic domain, and, in some isoforms, a C-terminal peroxisome targeting sequence. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]

ENSG00000280067 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.092 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031490.5. 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
	LONP2	NM_031490.5	MANE Select	c.1939-3517C>T		intron	N/A	NP_113678.2
	LONP2	NM_001348078.2		c.1939-3517C>T		intron	N/A	NP_001335007.1
	LONP2	NM_001300948.3		c.1807-3517C>T		intron	N/A	NP_001287877.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LONP2	ENST00000285737.9	TSL:1 MANE Select	c.1939-3517C>T		intron	N/A	ENSP00000285737.4
	LONP2	ENST00000535754.5	TSL:1	c.1807-3517C>T		intron	N/A	ENSP00000445426.1
	ENSG00000280067	ENST00000623817.1	TSL:6	n.2069G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12505 AN: 152058 Hom.: 556 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0539

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.0829

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0821 AC: 12501 AN: 152176 Hom.: 554 Cov.: 32 AF XY: 0.0824 AC XY: 6126 AN XY: 74374

African (AFR) AF: 0.0691 AC: 2870 AN: 41516

American (AMR) AF: 0.0773 AC: 1182 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3470

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5178

South Asian (SAS) AF: 0.0536 AC: 258 AN: 4816

European-Finnish (FIN) AF: 0.115 AC: 1212 AN: 10580

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0940 AC: 6390 AN: 68008

Other (OTH) AF: 0.0820 AC: 173 AN: 2110

Alfa AF: 0.0888 Hom.: 116

Bravo AF: 0.0776

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		0.041
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: rs16946122; hg19: chr16-48377901;