10-88727381-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080518.2(LIPK):​c.223+469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 184,084 control chromosomes in the GnomAD database, including 54,707 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 0.78 ( 46973 hom., cov: 33)
Exomes 𝑓: 0.69 ( 7734 hom. )

Consequence

LIPK
NM_001080518.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0100
Variant links:
Genes affected
LIPK (HGNC:23444): (lipase family member K) Predicted to enable lipoprotein lipase activity. Predicted to be involved in cornification. Predicted to be located in extracellular region. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]
KRT8P38 (HGNC:39872): (keratin 8 pseudogene 38)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LIPKNM_001080518.2 linkc.223+469C>T intron_variant Intron 3 of 9 ENST00000404190.3 NP_001073987.1 Q5VXJ0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LIPKENST00000404190.3 linkc.223+469C>T intron_variant Intron 3 of 9 1 NM_001080518.2 ENSP00000383900.1 Q5VXJ0
KRT8P38ENST00000441370.1 linkn.-104C>T upstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.777
AC:
118167
AN:
152100
Hom.:
46905
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.931
Gnomad AMI
AF:
0.852
Gnomad AMR
AF:
0.800
Gnomad ASJ
AF:
0.765
Gnomad EAS
AF:
0.996
Gnomad SAS
AF:
0.820
Gnomad FIN
AF:
0.710
Gnomad MID
AF:
0.810
Gnomad NFE
AF:
0.667
Gnomad OTH
AF:
0.783
GnomAD4 exome
AF:
0.685
AC:
21840
AN:
31866
Hom.:
7734
AF XY:
0.695
AC XY:
11177
AN XY:
16076
show subpopulations
Gnomad4 AFR exome
AF:
0.929
Gnomad4 AMR exome
AF:
0.815
Gnomad4 ASJ exome
AF:
0.748
Gnomad4 EAS exome
AF:
0.998
Gnomad4 SAS exome
AF:
0.795
Gnomad4 FIN exome
AF:
0.684
Gnomad4 NFE exome
AF:
0.646
Gnomad4 OTH exome
AF:
0.720
GnomAD4 genome
AF:
0.777
AC:
118295
AN:
152218
Hom.:
46973
Cov.:
33
AF XY:
0.781
AC XY:
58124
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.932
Gnomad4 AMR
AF:
0.801
Gnomad4 ASJ
AF:
0.765
Gnomad4 EAS
AF:
0.996
Gnomad4 SAS
AF:
0.820
Gnomad4 FIN
AF:
0.710
Gnomad4 NFE
AF:
0.667
Gnomad4 OTH
AF:
0.786
Alfa
AF:
0.722
Hom.:
9457
Bravo
AF:
0.792
Asia WGS
AF:
0.921
AC:
3204
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.5
DANN
Benign
0.21

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: rs378308; hg19: chr10-90487138; API