GeneBe

rs11248955

Positions:

Variant summary

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

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

2

Clinical Significance

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

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

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=-1.01).
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_multiple_submitters_no_conflicts, 2 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 Protein UniProt
LMF1NM_022773.4 linkuse as main transcriptc.514+131G>T intron_variant ENST00000262301.16 NP_073610.2
LMF1-AS1NR_110945.1 linkuse as main transcriptn.1066C>A non_coding_transcript_exon_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LMF1ENST00000262301.16 linkuse as main transcriptc.514+131G>T intron_variant 5 NM_022773.4 ENSP00000262301 P1Q96S06-1
LMF1-AS1ENST00000569574.1 linkuse as main transcriptn.1026C>A non_coding_transcript_exon_variant 3/33

Frequencies

GnomAD3 genomes
AF:
0.426
AC:
64702
AN:
152002
Hom.:
16892
Cov.:
33
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.:
34
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.:
33
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:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxAug 30, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

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.

Other links and lift over

dbSNP: rs11248955; hg19: chr16-984113; COSMIC: COSV51896082; API