16-971001-C-G

Variant names:

• chr16-971001-C-G
• rs13334376
• NM_001352019.2:c.-135+10144G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001352019.2(LMF1):​c.-135+10144G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000019 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000017 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LMF1 NM_001352019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 7 publications found

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 Gene-Disease associations (from GenCC):

• lipase deficiency, combined

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics

ENSG00000292433 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMF1	NM_022773.4	c.-21G>C		upstream_gene_variant		ENST00000262301.16	NP_073610.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMF1	ENST00000262301.16	c.-21G>C		upstream_gene_variant		5	NM_022773.4	ENSP00000262301.12

Frequencies

GnomAD3 genomes AF: 0.0000187 AC: 1 AN: 53386 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000344

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000171 AC: 1 AN: 585324 Hom.: 0 Cov.: 0 AF XY: 0.00000350 AC XY: 1 AN XY: 285450

African (AFR) AF: 0.00 AC: 0 AN: 5538

American (AMR) AF: 0.00 AC: 0 AN: 11008

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11104

East Asian (EAS) AF: 0.00 AC: 0 AN: 13790

South Asian (SAS) AF: 0.00 AC: 0 AN: 21412

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 18368

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1870

European-Non Finnish (NFE) AF: 0.00000209 AC: 1 AN: 478700

Other (OTH) AF: 0.00 AC: 0 AN: 23534

GnomAD4 genome AF: 0.0000187 AC: 1 AN: 53386 Hom.: 0 Cov.: 0 AF XY: 0.0000378 AC XY: 1 AN XY: 26446

African (AFR) AF: 0.00 AC: 0 AN: 7610

American (AMR) AF: 0.00 AC: 0 AN: 5388

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1864

East Asian (EAS) AF: 0.00 AC: 0 AN: 1962

South Asian (SAS) AF: 0.00 AC: 0 AN: 1344

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4888

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 156

European-Non Finnish (NFE) AF: 0.0000344 AC: 1 AN: 29090

Other (OTH) AF: 0.00 AC: 0 AN: 860

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.8
DANN	Benign	0.19
PhyloP100		0.0
PromoterAI		0.024	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13334376; hg19: chr16-1021001;