NM_001080518.2:c.669+2266T>A

Variant names:

• chr10-88734817-T-A
• rs391260
• NM_001080518.2:c.669+2266T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LIPK	NM_001080518.2	c.669+2266T>A		intron_variant	Intron 6 of 9	ENST00000404190.3	NP_001073987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPK	ENST00000404190.3	c.669+2266T>A		intron_variant	Intron 6 of 9	1	NM_001080518.2	ENSP00000383900.1

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

African (AFR) AF: 0.195 AC: 8110 AN: 41486

American (AMR) AF: 0.260 AC: 3969 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 907 AN: 3470

East Asian (EAS) AF: 0.365 AC: 1892 AN: 5184

South Asian (SAS) AF: 0.273 AC: 1316 AN: 4818

European-Finnish (FIN) AF: 0.155 AC: 1636 AN: 10568

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.214 AC: 14573 AN: 67972

Other (OTH) AF: 0.212 AC: 447 AN: 2110

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
PhyloP100		0.92
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs391260; hg19: chr10-90494574;