13-27584092-C-T

Position:

• chr13-27584092-C-T

Variant summary

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

The NM_153371.4(LNX2):​c.-100-2289G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0975 in 152,178 control chromosomes in the GnomAD database, including 1,024 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 0.098 (1024 hom., cov: 31)
• Consequence: LNX2 NM_153371.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

LNX2 (HGNC:20421): (ligand of numb-protein X 2) Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in protein ubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LNX2	NM_153371.4	c.-100-2289G>A		intron_variant		ENST00000316334.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LNX2	ENST00000316334.5	c.-100-2289G>A		intron_variant		1	NM_153371.4	P1
LNX2	ENST00000649248.1	c.-100-2289G>A		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 14844 AN: 152060 Hom.: 1024 Cov.: 31

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.0998

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

GnomAD4 genome AF: 0.0975 AC: 14841 AN: 152178 Hom.: 1024 Cov.: 31 AF XY: 0.100 AC XY: 7447 AN XY: 74406

Gnomad4 AFR AF: 0.0223

Gnomad4 AMR AF: 0.0808

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0901

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.0988

Alfa AF: 0.127 Hom.: 1787

Bravo AF: 0.0845

Asia WGS AF: 0.0450 AC: 158 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	0.19
DANN	Benign	0.46

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: rs9512755; hg19: chr13-28158229;