NM_005357.4:c.1420-880T>C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPE	NM_005357.4	c.1420-880T>C		intron_variant	Intron 2 of 9	ENST00000244289.9	NP_005348.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPE	ENST00000244289.9	c.1420-880T>C		intron_variant	Intron 2 of 9	1	NM_005357.4	ENSP00000244289.3

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

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.751

Alfa AF: 0.723 Hom.: 5410

Bravo AF: 0.781

Asia WGS AF: 0.960 AC: 3337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.36
DANN	Benign	0.53

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: rs1206034; hg19: chr19-42913354;