Variant rs11248955 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_022773.4(LMF1):c.514+131G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 1,557,000 control chromosomes in the GnomAD database, including 87,244 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 16947 hom., cov: 33)

Exomes 𝑓: 0.30 ( 70297 hom. )

Consequence

LMF1
NM_022773.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.10

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BP6

Variant 16-934113-C-A is Benign according to our data. Variant chr16-934113-C-A is described in ClinVar as [Benign]. Clinvar id is 1250664.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-934113-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMF1	NM_022773.4 linkuse as main transcript	c.514+131G>T		intron_variant		ENST00000262301.16
LMF1-AS1	NR_110945.1 linkuse as main transcript	n.1066C>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMF1	ENST00000262301.16 linkuse as main transcript	c.514+131G>T		intron_variant		5	NM_022773.4	P1	Q96S06-1
LMF1-AS1	ENST00000569574.1 linkuse as main transcript	n.1026C>A		non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64702

AN:

152002

Hom.:

16892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.739

Gnomad AMI

AF:

0.476

Gnomad AMR

AF:

0.413

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.377

Gnomad SAS

AF:

0.442

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.395

GnomAD3 exomes

AF:

0.363

AC:

64661

AN:

178176

Hom.:

13195

AF XY:

0.354

AC XY:

34450

AN XY:

97192

show subpopulations

Gnomad AFR exome

AF:

0.755

Gnomad AMR exome

AF:

0.443

Gnomad ASJ exome

AF:

0.246

Gnomad EAS exome

AF:

0.385

Gnomad SAS exome

AF:

0.425

Gnomad FIN exome

AF:

0.255

Gnomad NFE exome

AF:

0.283

Gnomad OTH exome

AF:

0.330

GnomAD4 exome

AF:

0.303

AC:

425432

AN:

1404880

Hom.:

70297

Cov.:

AF XY:

0.305

AC XY:

211943

AN XY:

695830

show subpopulations

Gnomad4 AFR exome

AF:

0.767

Gnomad4 AMR exome

AF:

0.443

Gnomad4 ASJ exome

AF:

0.247

Gnomad4 EAS exome

AF:

0.360

Gnomad4 SAS exome

AF:

0.423

Gnomad4 FIN exome

AF:

0.244

Gnomad4 NFE exome

AF:

0.275

Gnomad4 OTH exome

AF:

0.323

GnomAD4 genome

AF:

0.426

AC:

64816

AN:

152120

Hom.:

16947

Cov.:

AF XY:

0.423

AC XY:

31426

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.739

Gnomad4 AMR

AF:

0.413

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.377

Gnomad4 SAS

AF:

0.441

Gnomad4 FIN

AF:

0.238

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.392

Alfa

AF:

0.352

Hom.:

2133

Bravo

AF:

0.453

Asia WGS

AF:

0.446

AC:

1550

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 30, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.24

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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