10-88715962-A-G

Variant names:

• chr10-88715962-A-G
• rs413898
• NM_001080518.2:c.-11-8571A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080518.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPK	NM_001080518.2	MANE Select	c.-11-8571A>G		intron	N/A	NP_001073987.1
	LIPK	NM_001378091.1		c.-11-8571A>G		intron	N/A	NP_001365020.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPK	ENST00000404190.3	TSL:1 MANE Select	c.-11-8571A>G		intron	N/A	ENSP00000383900.1

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

African (AFR) AF: 0.937 AC: 38913 AN: 41516

American (AMR) AF: 0.807 AC: 12314 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2688 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5158 AN: 5178

South Asian (SAS) AF: 0.820 AC: 3947 AN: 4814

European-Finnish (FIN) AF: 0.709 AC: 7486 AN: 10556

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45991 AN: 67954

Other (OTH) AF: 0.796 AC: 1682 AN: 2112

Alfa AF: 0.668 Hom.: 2371

Bravo AF: 0.799

Asia WGS AF: 0.922 AC: 3198 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.86
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs413898; hg19: chr10-90475719;