rs7187700

Positions:

• chr16-962750-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.193+8038C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,136 control chromosomes in the GnomAD database, including 7,368 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 0.29 (7368 hom., cov: 32)
• Consequence: LMF1 NM_022773.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.714

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMF1	NM_022773.4	c.193+8038C>T		intron_variant		ENST00000262301.16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMF1	ENST00000262301.16	c.193+8038C>T		intron_variant		5	NM_022773.4	P1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44104 AN: 152018 Hom.: 7353 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0960

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.290 AC: 44161 AN: 152136 Hom.: 7368 Cov.: 32 AF XY: 0.288 AC XY: 21433 AN XY: 74378

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0951

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.264

Alfa AF: 0.235 Hom.: 6978

Bravo AF: 0.294

Asia WGS AF: 0.244 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.63

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: rs7187700; hg19: chr16-1012750;