rs1544799

chr16-935717-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022773.4(LMF1):c.504-1463C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,142 control chromosomes in the GnomAD database, including 16,604 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (16604 hom., cov: 34)
• Consequence: LMF1 NM_022773.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMF1	NM_022773.4	c.504-1463C>T		intron_variant		ENST00000262301.16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMF1	ENST00000262301.16	c.504-1463C>T		intron_variant		5	NM_022773.4	P1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65030 AN: 152024 Hom.: 16554 Cov.: 34

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.401

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.428 AC: 65137 AN: 152142 Hom.: 16604 Cov.: 34 AF XY: 0.426 AC XY: 31699 AN XY: 74378

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.398

Alfa AF: 0.386 Hom.: 2495

Bravo AF: 0.451

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.6
Dann	Benign	0.59

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

Other links and lift over

dbSNP: rs1544799; hg19: chr16-985717;