19-42409202-A-G

Variant names:

• chr19-42409202-A-G
• rs1206034
• NM_005357.4:c.1420-880T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005357.4(LIPE):​c.1420-880T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 151,658 control chromosomes in the GnomAD database, including 46,115 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 0.77 (46115 hom., cov: 28)
• Consequence: LIPE NM_005357.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 5 publications found

Genes affected

LIPE (HGNC:6621): (lipase E, hormone sensitive type) The protein encoded by this gene has a long and a short form, generated by use of alternative translational start codons. The long form is expressed in steroidogenic tissues such as testis, where it converts cholesteryl esters to free cholesterol for steroid hormone production. The short form is expressed in adipose tissue, among others, where it hydrolyzes stored triglycerides to free fatty acids. [provided by RefSeq, Jul 2008]

LIPE-AS1 (HGNC:48589): (LIPE antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005357.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPE	NM_005357.4	MANE Select	c.1420-880T>C		intron	N/A	NP_005348.2
	LIPE	NM_001416100.1		c.655-880T>C		intron	N/A	NP_001403029.1
	LIPE	NM_001416101.1		c.655-880T>C		intron	N/A	NP_001403030.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPE	ENST00000244289.9	TSL:1 MANE Select	c.1420-880T>C		intron	N/A	ENSP00000244289.3
	LIPE	ENST00000599783.5	TSL:1	c.655-880T>C		intron	N/A	ENSP00000469990.1
	LIPE-AS1	ENST00000594624.8	TSL:1	n.105+11978A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116215 AN: 151540 Hom.: 46051 Cov.: 28

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.767 AC: 116340 AN: 151658 Hom.: 46115 Cov.: 28 AF XY: 0.774 AC XY: 57333 AN XY: 74096

African (AFR) AF: 0.939 AC: 38830 AN: 41346

American (AMR) AF: 0.778 AC: 11844 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2671 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5115 AN: 5128

South Asian (SAS) AF: 0.929 AC: 4467 AN: 4810

European-Finnish (FIN) AF: 0.680 AC: 7150 AN: 10522

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43900 AN: 67856

Other (OTH) AF: 0.751 AC: 1581 AN: 2106

Alfa AF: 0.804 Hom.: 11556

Bravo AF: 0.781

Asia WGS AF: 0.960 AC: 3337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.36
DANN	Benign	0.53
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1206034; hg19: chr19-42913354;