rs13334376
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001352019.2(LMF1):c.-135+10144G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00693 in 638,546 control chromosomes in the GnomAD database, including 164 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00075 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0075 ( 164 hom. )
Consequence
LMF1
NM_001352019.2 intron
NM_001352019.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 16-971001-C-A is Benign according to our data. Variant chr16-971001-C-A is described in ClinVar as [Benign]. Clinvar id is 1242679.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000749 (40/53398) while in subpopulation AFR AF= 0.00223 (17/7620). AF 95% confidence interval is 0.00142. There are 0 homozygotes in gnomad4. There are 18 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 237 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMF1 | NM_022773.4 | upstream_gene_variant | ENST00000262301.16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMF1 | ENST00000262301.16 | upstream_gene_variant | 5 | NM_022773.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000749 AC: 40AN: 53384Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.0761 AC: 5608AN: 73662Hom.: 237 AF XY: 0.0733 AC XY: 3065AN XY: 41818
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GnomAD4 exome AF: 0.00750 AC: 4387AN: 585148Hom.: 164 Cov.: 0 AF XY: 0.00838 AC XY: 2392AN XY: 285380
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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 | Nov 26, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at