rs11266282

Variant names:

• chrX-37591763-A-T
• rs11266282
• NM_001170331.2:c.573+19320A>T

Variant summary

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

The NM_001170331.2(LANCL3):​c.573+19320A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.20 (1682 hom., 5313 hem., cov: 20)
• Consequence: LANCL3 NM_001170331.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 2 publications found

Genes affected

LANCL3 (HGNC:24767): (LanC like family member 3) Predicted to be involved in carbohydrate metabolic process. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000250349 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LANCL3	NM_001170331.2	c.573+19320A>T		intron_variant	Intron 1 of 4	ENST00000378619.4	NP_001163802.1
LANCL3	NM_198511.3	c.573+19320A>T		intron_variant	Intron 1 of 5		NP_940913.1
LANCL3	XM_011543904.3	c.27+18896A>T		intron_variant	Intron 1 of 4		XP_011542206.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LANCL3	ENST00000378619.4	c.573+19320A>T		intron_variant	Intron 1 of 4	1	NM_001170331.2	ENSP00000367882.4
ENSG00000250349	ENST00000465127.1	c.171+165763A>T		intron_variant	Intron 3 of 8	5		ENSP00000417050.1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 20487 AN: 103074 Hom.: 1682 Cov.: 20

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.199 AC: 20483 AN: 103112 Hom.: 1682 Cov.: 20 AF XY: 0.196 AC XY: 5313 AN XY: 27156

African (AFR) AF: 0.108 AC: 2853 AN: 26359

American (AMR) AF: 0.274 AC: 2665 AN: 9726

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 626 AN: 2559

East Asian (EAS) AF: 0.227 AC: 699 AN: 3079

South Asian (SAS) AF: 0.129 AC: 294 AN: 2279

European-Finnish (FIN) AF: 0.190 AC: 994 AN: 5218

Middle Eastern (MID) AF: 0.120 AC: 25 AN: 208

European-Non Finnish (NFE) AF: 0.230 AC: 11865 AN: 51604

Other (OTH) AF: 0.218 AC: 310 AN: 1425

Alfa AF: 0.186 Hom.: 911

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		0.0090
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: rs11266282; hg19: chrX-37451016;