dbSNP rs3751667: LMF1:p.Thr102Thr (chr16-954554-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_022773.4(LMF1):c.306G>A(p.Thr102Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,612,686 control chromosomes in the GnomAD database, including 56,067 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 7115 hom., cov: 33)

Exomes 𝑓: 0.25 ( 48952 hom. )

Consequence

LMF1
NM_022773.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -1.13

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 16-954554-C-T is Benign according to our data. Variant chr16-954554-C-T is described in ClinVar as [Benign]. Clinvar id is 1246959.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-954554-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.13 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMF1	NM_022773.4 link	c.306G>A	p.Thr102Thr	synonymous_variant	Exon 2 of 11	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.306G>A	p.Thr102Thr	synonymous_variant	Exon 2 of 11	5	NM_022773.4	ENSP00000262301.12		Q96S06-1

Frequencies

GnomAD3 genomes

AF:

0.289

AC:

43957

AN:

152038

Hom.:

7102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.402

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.278

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.406

Gnomad SAS

AF:

0.438

Gnomad FIN

AF:

0.130

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.277

GnomAD3 exomes

AF:

0.277

AC:

68629

AN:

247618

Hom.:

10548

AF XY:

0.280

AC XY:

37623

AN XY:

134596

show subpopulations

Gnomad AFR exome

AF:

0.406

Gnomad AMR exome

AF:

0.288

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.407

Gnomad SAS exome

AF:

0.429

Gnomad FIN exome

AF:

0.139

Gnomad NFE exome

AF:

0.227

Gnomad OTH exome

AF:

0.258

GnomAD4 exome

AF:

0.250

AC:

365474

AN:

1460530

Hom.:

48952

Cov.:

AF XY:

0.255

AC XY:

184971

AN XY:

726506

show subpopulations

Gnomad4 AFR exome

AF:

0.415

Gnomad4 AMR exome

AF:

0.289

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.392

Gnomad4 SAS exome

AF:

0.421

Gnomad4 FIN exome

AF:

0.152

Gnomad4 NFE exome

AF:

0.230

Gnomad4 OTH exome

AF:

0.263

GnomAD4 genome

AF:

0.289

AC:

44011

AN:

152156

Hom.:

7115

Cov.:

AF XY:

0.287

AC XY:

21343

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.402

Gnomad4 AMR

AF:

0.278

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.406

Gnomad4 SAS

AF:

0.437

Gnomad4 FIN

AF:

0.130

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.276

Alfa

AF:

0.246

Hom.:

7991

Bravo

AF:

0.301

Asia WGS

AF:

0.414

AC:

1441

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

- -

Cardiovascular phenotype

Benign:1

Feb 03, 2019

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.64

DANN

Benign

0.29

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