Variant chr16-854395-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_022773.4(LMF1):c.*137G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00208 in 914,578 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0074 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0010 ( 7 hom. )

Consequence

LMF1
NM_022773.4 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.22

Variant links:

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 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 16-854395-C-T is Benign according to our data. Variant chr16-854395-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1213201.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00742 (1129/152214) while in subpopulation AFR AF= 0.0248 (1029/41516). AF 95% confidence interval is 0.0235. There are 6 homozygotes in gnomad4. There are 522 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMF1	NM_022773.4 linkuse as main transcript	c.*137G>A		3_prime_UTR_variant	11/11	ENST00000262301.16

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMF1	ENST00000262301.16 linkuse as main transcript	c.*137G>A	3_prime_UTR_variant	11/11	5	NM_022773.4	P1	Q96S06-1
	ENST00000655150.1 linkuse as main transcript	n.632-6637C>T	intron_variant, non_coding_transcript_variant
LMF1	ENST00000543238.5 linkuse as main transcript	c.*137G>A	3_prime_UTR_variant	8/8	2			Q96S06-2
LMF1	ENST00000545827.6 linkuse as main transcript	c.*1378G>A	3_prime_UTR_variant, NMD_transcript_variant	12/12	2

Frequencies

GnomAD3 genomes

AF:

0.00742

AC:

1128

AN:

152096

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0248

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00320

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000529

Gnomad OTH

AF:

0.00479

GnomAD3 exomes

AF:

0.00187

AC:

225

AN:

120566

Hom.:

AF XY:

0.00138

AC XY:

AN XY:

65248

show subpopulations

Gnomad AFR exome

AF:

0.0245

Gnomad AMR exome

AF:

0.00165

Gnomad ASJ exome

AF:

0.000750

Gnomad EAS exome

AF:

0.0000980

Gnomad SAS exome

AF:

0.0000517

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000504

Gnomad OTH exome

AF:

0.00109

GnomAD4 exome

AF:

0.00101

AC:

769

AN:

762364

Hom.:

Cov.:

AF XY:

0.000839

AC XY:

332

AN XY:

395836

show subpopulations

Gnomad4 AFR exome

AF:

0.0229

Gnomad4 AMR exome

AF:

0.00160

Gnomad4 ASJ exome

AF:

0.000598

Gnomad4 EAS exome

AF:

0.0000305

Gnomad4 SAS exome

AF:

0.0000939

Gnomad4 FIN exome

AF:

0.0000306

Gnomad4 NFE exome

AF:

0.000344

Gnomad4 OTH exome

AF:

0.00200

GnomAD4 genome

AF:

0.00742

AC:

1129

AN:

152214

Hom.:

Cov.:

AF XY:

0.00701

AC XY:

522

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.0248

Gnomad4 AMR

AF:

0.00320

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.000529

Gnomad4 OTH

AF:

0.00474

Alfa

AF:

0.00373

Hom.:

Bravo

AF:

0.00788

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.1

DANN

Benign

0.49

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over