Variant 16-954694-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_022773.4(LMF1):c.194-28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 1,559,114 control chromosomes in the GnomAD database, including 138,846 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 20609 hom., cov: 34)

Exomes 𝑓: 0.40 ( 118237 hom. )

Consequence

LMF1
NM_022773.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.15

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 (HGNC:):

LMF1 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=-0.92).

BP6

Variant 16-954694-A-G is Benign according to our data. Variant chr16-954694-A-G is described in ClinVar as [Benign]. Clinvar id is 1275485.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-954694-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMF1	NM_022773.4 linkuse as main transcript	c.194-28T>C		intron_variant		ENST00000262301.16	NP_073610.2	Q96S06-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMF1	ENST00000262301.16 linkuse as main transcript	c.194-28T>C		intron_variant		5	NM_022773.4	ENSP00000262301.12		Q96S06-1

Frequencies

GnomAD3 genomes

AF:

0.493

AC:

74904

AN:

152052

Hom.:

20560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.742

Gnomad AMI

AF:

0.477

Gnomad AMR

AF:

0.477

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.397

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.309

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.382

Gnomad OTH

AF:

0.469

GnomAD3 exomes

AF:

0.444

AC:

90811

AN:

204676

Hom.:

21368

AF XY:

0.438

AC XY:

48105

AN XY:

109826

show subpopulations

Gnomad AFR exome

AF:

0.752

Gnomad AMR exome

AF:

0.498

Gnomad ASJ exome

AF:

0.322

Gnomad EAS exome

AF:

0.402

Gnomad SAS exome

AF:

0.594

Gnomad FIN exome

AF:

0.324

Gnomad NFE exome

AF:

0.380

Gnomad OTH exome

AF:

0.418

GnomAD4 exome

AF:

0.402

AC:

565134

AN:

1406944

Hom.:

118237

Cov.:

AF XY:

0.405

AC XY:

280881

AN XY:

693888

show subpopulations

Gnomad4 AFR exome

AF:

0.765

Gnomad4 AMR exome

AF:

0.499

Gnomad4 ASJ exome

AF:

0.319

Gnomad4 EAS exome

AF:

0.380

Gnomad4 SAS exome

AF:

0.574

Gnomad4 FIN exome

AF:

0.327

Gnomad4 NFE exome

AF:

0.380

Gnomad4 OTH exome

AF:

0.413

GnomAD4 genome

AF:

0.493

AC:

75011

AN:

152170

Hom.:

20609

Cov.:

AF XY:

0.489

AC XY:

36394

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.742

Gnomad4 AMR

AF:

0.478

Gnomad4 ASJ

AF:

0.333

Gnomad4 EAS

AF:

0.397

Gnomad4 SAS

AF:

0.594

Gnomad4 FIN

AF:

0.309

Gnomad4 NFE

AF:

0.383

Gnomad4 OTH

AF:

0.468

Alfa

AF:

0.387

Hom.:

15261

Bravo

AF:

0.512

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 16, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.0060

DANN

Benign

0.22

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