rs391260

Positions:

• chr10-88734817-T-A
• chr10-88734817-T-C

Variant summary

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

The NM_001080518.2(LIPK):​c.669+2266T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,092 control chromosomes in the GnomAD database, including 3,790 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 0.22 (3790 hom., cov: 32)
• Consequence: LIPK NM_001080518.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.921

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPK	NM_001080518.2	c.669+2266T>A		intron_variant		ENST00000404190.3	NP_001073987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPK	ENST00000404190.3	c.669+2266T>A		intron_variant		1	NM_001080518.2	ENSP00000383900	P1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33082 AN: 151974 Hom.: 3776 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.218 AC: 33129 AN: 152092 Hom.: 3790 Cov.: 32 AF XY: 0.218 AC XY: 16204 AN XY: 74344

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.212

Alfa AF: 0.219 Hom.: 446

Bravo AF: 0.224

Asia WGS AF: 0.307 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.80

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: rs391260; hg19: chr10-90494574;