chrX-119009855-C-T

Position:

• chrX-119009855-C-T

Variant summary

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

The NM_001031855.3(LONRF3):​c.1652+608C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 110,170 control chromosomes in the GnomAD database, including 3,970 homozygotes. There are 9,590 hemizygotes in GnomAD. 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 0.31 (3970 hom., 9590 hem., cov: 22)
• Consequence: LONRF3 NM_001031855.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

LONRF3 (HGNC:21152): (LON peptidase N-terminal domain and ring finger 3) The protein encoded by this gene contains a RING finger domain, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. Multiple alternatively spliced transcript variants have been suggested, but their full length natures are not clear. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LONRF3	NM_001031855.3	c.1652+608C>T		intron_variant		ENST00000371628.8	NP_001027026.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LONRF3	ENST00000371628.8	c.1652+608C>T		intron_variant		1	NM_001031855.3	ENSP00000360690.3

Frequencies

GnomAD3 genomes AF: 0.305 AC: 33598 AN: 110113 Hom.: 3969 Cov.: 22 AF XY: 0.295 AC XY: 9570 AN XY: 32401

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.422

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.343

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.305 AC: 33621 AN: 110170 Hom.: 3970 Cov.: 22 AF XY: 0.295 AC XY: 9590 AN XY: 32468

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.0767

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.346

Alfa AF: 0.323 Hom.: 2089

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.051
DANN	Benign	0.80

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: rs4825625; hg19: chrX-118143818;