Genetic Variant LANCL3:p.Ala152Thr (chrX-37572324-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001170331.2(LANCL3):c.454G>A(p.Ala152Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000253 in 1,161,514 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 79 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0011 ( 0 hom., 32 hem., cov: 23)

Exomes 𝑓: 0.00016 ( 0 hom. 47 hem. )

Consequence

LANCL3
NM_001170331.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.18

Variant links:

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]

LANCL3 links:

ENSG00000250349 (HGNC:):

ENSG00000250349 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008877426).

BS2

High Hemizygotes in GnomAd4 at 32 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LANCL3	NM_001170331.2 link	c.454G>A	p.Ala152Thr	missense_variant	Exon 1 of 5	ENST00000378619.4	NP_001163802.1	Q6ZV70-1
LANCL3	NM_198511.3 link	c.454G>A	p.Ala152Thr	missense_variant	Exon 1 of 6		NP_940913.1	Q6ZV70-2
LANCL3	XM_011543904.3 link	c.-517G>A		upstream_gene_variant			XP_011542206.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
LANCL3	ENST00000378619.4 link	c.454G>A	p.Ala152Thr	missense_variant	Exon 1 of 5	1	NM_001170331.2	ENSP00000367882.4	Q6ZV70-1
LANCL3	ENST00000378621.7 link	c.454G>A	p.Ala152Thr	missense_variant	Exon 1 of 6	1		ENSP00000367885.3	Q6ZV70-2
ENSG00000250349	ENST00000465127.1 link	c.171+146324G>A		intron_variant	Intron 3 of 8	5		ENSP00000417050.1	B4E171
LANCL3	ENST00000614025.4 link	c.454G>A	p.Ala152Thr	missense_variant	Exon 1 of 5	2		ENSP00000479231.1	Q6ZV70-2

Frequencies

GnomAD3 genomes

AF:

0.00108

AC:

121

AN:

112246

Hom.:

Cov.:

AF XY:

0.000930

AC XY:

AN XY:

34396

show subpopulations

Gnomad AFR

AF:

0.00350

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000650

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00837

Gnomad NFE

AF:

0.0000377

Gnomad OTH

AF:

0.00133

GnomAD3 exomes

AF:

0.000269

AC:

AN:

103991

Hom.:

AF XY:

0.000188

AC XY:

AN XY:

37299

show subpopulations

Gnomad AFR exome

AF:

0.00357

Gnomad AMR exome

AF:

0.000155

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000711

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000128

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000165

AC:

173

AN:

1049214

Hom.:

Cov.:

AF XY:

0.000137

AC XY:

AN XY:

341920

show subpopulations

Gnomad4 AFR exome

AF:

0.00478

Gnomad4 AMR exome

AF:

0.000179

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000201

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000293

Gnomad4 OTH exome

AF:

0.000497

GnomAD4 genome

AF:

0.00108

AC:

121

AN:

112300

Hom.:

Cov.:

AF XY:

0.000929

AC XY:

AN XY:

34460

show subpopulations

Gnomad4 AFR

AF:

0.00349

Gnomad4 AMR

AF:

0.000649

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000377

Gnomad4 OTH

AF:

0.00131

Alfa

AF:

0.000781

Hom.:

Bravo

AF:

0.00125

ExAC

AF:

0.0000859

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Jun 09, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.454G>A (p.A152T) alteration is located in exon 1 (coding exon 1) of the LANCL3 gene. This alteration results from a G to A substitution at nucleotide position 454, causing the alanine (A) at amino acid position 152 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.016

.;.;T

FATHMM_MKL

Benign

0.64

LIST_S2

Benign

0.81

T;.;T

M_CAP

Benign

0.084

MetaRNN

Benign

0.0089

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.20

N;N;N

PrimateAI

Pathogenic

0.86

PROVEAN

Benign

-0.36

.;N;N

REVEL

Benign

0.057

Sift

Benign

0.27

.;T;T

Sift4G

Benign

0.42

T;T;T

Polyphen

0.0040

B;B;B

Vest4

0.092

MVP

0.27

MPC

0.51

ClinPred

0.018

GERP RS

3.2

Varity_R

0.14

gMVP

0.079

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over