chr19-42402121-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005357.4(LIPE):​c.2968-46G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.098 in 1,420,750 control chromosomes in the GnomAD database, including 7,656 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.082 ( 649 hom., cov: 31)
Exomes 𝑓: 0.10 ( 7007 hom. )

Consequence

LIPE
NM_005357.4 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0160
Variant links:
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]

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=-0.84).
BP6
Variant 19-42402121-C-G is Benign according to our data. Variant chr19-42402121-C-G is described in ClinVar as [Benign]. Clinvar id is 1234041.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LIPENM_005357.4 linkuse as main transcriptc.2968-46G>C intron_variant ENST00000244289.9 NP_005348.2 Q05469-1A8K8W7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LIPEENST00000244289.9 linkuse as main transcriptc.2968-46G>C intron_variant 1 NM_005357.4 ENSP00000244289.3 Q05469-1

Frequencies

GnomAD3 genomes
AF:
0.0825
AC:
12546
AN:
152074
Hom.:
653
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0319
Gnomad AMI
AF:
0.100
Gnomad AMR
AF:
0.125
Gnomad ASJ
AF:
0.0914
Gnomad EAS
AF:
0.0407
Gnomad SAS
AF:
0.196
Gnomad FIN
AF:
0.0740
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.0986
Gnomad OTH
AF:
0.0934
GnomAD3 exomes
AF:
0.121
AC:
5185
AN:
42746
Hom.:
388
AF XY:
0.123
AC XY:
2756
AN XY:
22358
show subpopulations
Gnomad AFR exome
AF:
0.0346
Gnomad AMR exome
AF:
0.158
Gnomad ASJ exome
AF:
0.110
Gnomad EAS exome
AF:
0.0468
Gnomad SAS exome
AF:
0.218
Gnomad FIN exome
AF:
0.0741
Gnomad NFE exome
AF:
0.128
Gnomad OTH exome
AF:
0.114
GnomAD4 exome
AF:
0.0998
AC:
126655
AN:
1268558
Hom.:
7007
Cov.:
34
AF XY:
0.102
AC XY:
62769
AN XY:
614198
show subpopulations
Gnomad4 AFR exome
AF:
0.0301
Gnomad4 AMR exome
AF:
0.144
Gnomad4 ASJ exome
AF:
0.0899
Gnomad4 EAS exome
AF:
0.0309
Gnomad4 SAS exome
AF:
0.187
Gnomad4 FIN exome
AF:
0.0702
Gnomad4 NFE exome
AF:
0.0986
Gnomad4 OTH exome
AF:
0.101
GnomAD4 genome
AF:
0.0823
AC:
12532
AN:
152192
Hom.:
649
Cov.:
31
AF XY:
0.0842
AC XY:
6263
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.0318
Gnomad4 AMR
AF:
0.125
Gnomad4 ASJ
AF:
0.0914
Gnomad4 EAS
AF:
0.0406
Gnomad4 SAS
AF:
0.195
Gnomad4 FIN
AF:
0.0740
Gnomad4 NFE
AF:
0.0986
Gnomad4 OTH
AF:
0.0919
Alfa
AF:
0.0907
Hom.:
89
Bravo
AF:
0.0835
Asia WGS
AF:
0.115
AC:
402
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJun 20, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
6.9
DANN
Benign
0.55

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.

Other links and lift over

dbSNP: rs35639038; hg19: chr19-42906273; API