chr16-854551-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_022773.4(LMF1):c.1685C>G(p.Pro562Arg) variant causes a missense change. The variant allele was found at a frequency of 0.02 in 1,608,040 control chromosomes in the GnomAD database, including 1,477 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.026 ( 225 hom., cov: 33)
Exomes 𝑓: 0.019 ( 1252 hom. )
Consequence
LMF1
NM_022773.4 missense
NM_022773.4 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: 4.50
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017978847).
BP6
?
Variant 16-854551-G-C is Benign according to our data. Variant chr16-854551-G-C is described in ClinVar as [Benign]. Clinvar id is 1277320.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMF1 | NM_022773.4 | c.1685C>G | p.Pro562Arg | missense_variant | 11/11 | ENST00000262301.16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMF1 | ENST00000262301.16 | c.1685C>G | p.Pro562Arg | missense_variant | 11/11 | 5 | NM_022773.4 | P1 | |
ENST00000655150.1 | n.632-6481G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0261 AC: 3977AN: 152166Hom.: 222 Cov.: 33
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GnomAD3 exomes AF: 0.0468 AC: 11050AN: 236352Hom.: 754 AF XY: 0.0412 AC XY: 5357AN XY: 129908
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GnomAD4 exome AF: 0.0193 AC: 28119AN: 1455756Hom.: 1252 Cov.: 31 AF XY: 0.0197 AC XY: 14250AN XY: 724096
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GnomAD4 genome ? AF: 0.0262 AC: 3984AN: 152284Hom.: 225 Cov.: 33 AF XY: 0.0300 AC XY: 2231AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 17, 2018 | This variant is associated with the following publications: (PMID: 27108409, 22239554, 25817768, 30420299) - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2019 | 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
P;.;.
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at