13-27615843-C-T

Variant names:

• chr13-27615843-C-T
• rs534150
• NM_153371.4:c.-101+4532G>A

Variant summary

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

The NM_153371.4(LNX2):​c.-101+4532G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,990 control chromosomes in the GnomAD database, including 19,997 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 0.50 (19997 hom., cov: 31)
• Consequence: LNX2 NM_153371.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777
• Publications: 8 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153371.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNX2	NM_153371.4	MANE Select	c.-101+4532G>A		intron	N/A	NP_699202.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNX2	ENST00000316334.5	TSL:1 MANE Select	c.-101+4532G>A		intron	N/A	ENSP00000325929.3
	LNX2	ENST00000869675.1		c.-101+5196G>A		intron	N/A	ENSP00000539734.1
	LNX2	ENST00000869676.1		c.-101+4180G>A		intron	N/A	ENSP00000539735.1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75362 AN: 151872 Hom.: 19984 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.496 AC: 75414 AN: 151990 Hom.: 19997 Cov.: 31 AF XY: 0.504 AC XY: 37450 AN XY: 74300

African (AFR) AF: 0.302 AC: 12496 AN: 41432

American (AMR) AF: 0.575 AC: 8790 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3468

East Asian (EAS) AF: 0.544 AC: 2812 AN: 5166

South Asian (SAS) AF: 0.606 AC: 2920 AN: 4820

European-Finnish (FIN) AF: 0.642 AC: 6789 AN: 10578

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38154 AN: 67932

Other (OTH) AF: 0.494 AC: 1044 AN: 2112

Alfa AF: 0.548 Hom.: 21293

Bravo AF: 0.482

Asia WGS AF: 0.601 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.34
PhyloP100		-0.78
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: rs534150; hg19: chr13-28189980;