rs405635

chr10-88729900-G-Achr10-88729900-G-Cchr10-88729900-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIPK	NM_001080518.2	c.224-1083G>A		intron_variant		ENST00000404190.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPK	ENST00000404190.3	c.224-1083G>A		intron_variant		1	NM_001080518.2	P1

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

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.257

Alfa AF: 0.159 Hom.: 363

Bravo AF: 0.255

Asia WGS AF: 0.319 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.010
Dann	Benign	0.32

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: rs405635; hg19: chr10-90489657;