chr10-88729900-G-A

Variant names:

• chr10-88729900-G-A
• rs405635
• NM_001080518.2:c.224-1083G>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.224-1083G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,064 control chromosomes in the GnomAD database, including 4,829 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 0.25 (4829 hom., cov: 32)
• Consequence: LIPK NM_001080518.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 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.224-1083G>A		intron	N/A	NP_001073987.1
	LIPK	NM_001378091.1		c.224-1182G>A		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.224-1083G>A		intron	N/A	ENSP00000383900.1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37466 AN: 151946 Hom.: 4813 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.247 AC: 37517 AN: 152064 Hom.: 4829 Cov.: 32 AF XY: 0.246 AC XY: 18314 AN XY: 74352

African (AFR) AF: 0.217 AC: 8999 AN: 41484

American (AMR) AF: 0.300 AC: 4585 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1878 AN: 5168

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4824

European-Finnish (FIN) AF: 0.158 AC: 1670 AN: 10572

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16883 AN: 67952

Other (OTH) AF: 0.257 AC: 543 AN: 2112

Alfa AF: 0.160 Hom.: 378

Bravo AF: 0.255

Asia WGS AF: 0.319 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.010
DANN	Benign	0.32
PhyloP100		-0.49
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: rs405635; hg19: chr10-90489657;