Genetic Variant LMF1:c.514+241C>G (chr16-934003-G-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001352018.2(LMF1):c.103C>G(p.Arg35Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 1,480,490 control chromosomes in the GnomAD database, including 5,645 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.072 ( 457 hom., cov: 33)

Exomes 𝑓: 0.085 ( 5188 hom. )

Consequence

LMF1
NM_001352018.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.04

Variant links:

Genes affected

LMF1 (HGNC:14154): (lipase maturation factor 1) Involved in triglyceride metabolic process. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum membrane. Implicated in familial lipase maturation factor 1 deficiency. [provided by Alliance of Genome Resources, Apr 2022]

LMF1 links:

LMF1-AS1 (HGNC:50469): (LMF1 antisense RNA 1)

LMF1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.06).

BP6

Variant 16-934003-G-C is Benign according to our data. Variant chr16-934003-G-C is described in ClinVar as [Benign]. Clinvar id is 1271022.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-934003-G-C is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMF1	NM_022773.4 link	c.514+241C>G		intron_variant	Intron 3 of 10	ENST00000262301.16	NP_073610.2	Q96S06-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMF1	ENST00000262301.16 link	c.514+241C>G		intron_variant	Intron 3 of 10	5	NM_022773.4	ENSP00000262301.12		Q96S06-1

Frequencies

GnomAD3 genomes

AF:

0.0725

AC:

11024

AN:

152146

Hom.:

456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0544

Gnomad AMI

AF:

0.0396

Gnomad AMR

AF:

0.0477

Gnomad ASJ

AF:

0.0700

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0538

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0914

Gnomad OTH

AF:

0.0750

GnomAD3 exomes

AF:

0.0648

AC:

8340

AN:

128766

Hom.:

364

AF XY:

0.0654

AC XY:

4600

AN XY:

70356

show subpopulations

Gnomad AFR exome

AF:

0.0542

Gnomad AMR exome

AF:

0.0385

Gnomad ASJ exome

AF:

0.0684

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0606

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.0887

Gnomad OTH exome

AF:

0.0766

GnomAD4 exome

AF:

0.0847

AC:

112500

AN:

1328226

Hom.:

5188

Cov.:

AF XY:

0.0841

AC XY:

54993

AN XY:

653858

show subpopulations

Gnomad4 AFR exome

AF:

0.0525

Gnomad4 AMR exome

AF:

0.0406

Gnomad4 ASJ exome

AF:

0.0629

Gnomad4 EAS exome

AF:

0.0000933

Gnomad4 SAS exome

AF:

0.0588

Gnomad4 FIN exome

AF:

0.118

Gnomad4 NFE exome

AF:

0.0916

Gnomad4 OTH exome

AF:

0.0772

GnomAD4 genome

AF:

0.0724

AC:

11030

AN:

152264

Hom.:

457

Cov.:

AF XY:

0.0718

AC XY:

5347

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0544

Gnomad4 AMR

AF:

0.0477

Gnomad4 ASJ

AF:

0.0700

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0537

Gnomad4 FIN

AF:

0.105

Gnomad4 NFE

AF:

0.0914

Gnomad4 OTH

AF:

0.0747

Alfa

AF:

0.0798

Hom.:

Bravo

AF:

0.0661

Asia WGS

AF:

0.0260

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Aug 30, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

LMF1-related disorder

Benign:1

Apr 04, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.15

DANN

Benign

0.31

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