rs413898

chr10-88715962-A-Gchr10-88715962-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080518.2(LIPK):c.-11-8571A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,064 control chromosomes in the GnomAD database, including 47,692 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 (47692 hom., cov: 32)
• Consequence: LIPK NM_001080518.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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/exons	MANE	UniProt
LIPK	NM_001080518.2	c.-11-8571A>G		intron_variant		ENST00000404190.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPK	ENST00000404190.3	c.-11-8571A>G		intron_variant		1	NM_001080518.2	P1

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119077 AN: 151946 Hom.: 47626 Cov.: 32

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.784 AC: 119203 AN: 152064 Hom.: 47692 Cov.: 32 AF XY: 0.787 AC XY: 58507 AN XY: 74308

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.796

Alfa AF: 0.644 Hom.: 2023

Bravo AF: 0.799

Asia WGS AF: 0.922 AC: 3198 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.3
Dann	Benign	0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs413898; hg19: chr10-90475719;