chr13-27600204-G-A

Variant names:

• chr13-27600204-G-A
• rs1886204
• NM_153371.4:c.-100-18401C>T

Variant summary

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

The NM_153371.4(LNX2):​c.-100-18401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,960 control chromosomes in the GnomAD database, including 10,861 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 0.36 (10861 hom., cov: 32)
• Consequence: LNX2 NM_153371.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 4 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=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNX2	NM_153371.4	c.-100-18401C>T		intron_variant	Intron 1 of 9	ENST00000316334.5	NP_699202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNX2	ENST00000316334.5	c.-100-18401C>T		intron_variant	Intron 1 of 9	1	NM_153371.4	ENSP00000325929.3
LNX2	ENST00000649248.1	c.-101+6526C>T		intron_variant	Intron 2 of 10			ENSP00000497224.1

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55374 AN: 151842 Hom.: 10856 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.365 AC: 55419 AN: 151960 Hom.: 10861 Cov.: 32 AF XY: 0.361 AC XY: 26798 AN XY: 74278

African (AFR) AF: 0.511 AC: 21156 AN: 41434

American (AMR) AF: 0.317 AC: 4839 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1261 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1802 AN: 5154

South Asian (SAS) AF: 0.318 AC: 1529 AN: 4814

European-Finnish (FIN) AF: 0.273 AC: 2885 AN: 10550

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20780 AN: 67948

Other (OTH) AF: 0.360 AC: 760 AN: 2110

Alfa AF: 0.237 Hom.: 656

Bravo AF: 0.375

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	0.58
DANN	Benign	0.36
PhyloP100		-0.79
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: rs1886204; hg19: chr13-28174341;