rs412927

chr10-88727523-A-G

Variant summary

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

The NM_001080518.2(LIPK):c.223+611A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 158,952 control chromosomes in the GnomAD database, including 48,639 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 (46894 hom., cov: 31)
  • Exomes 𝑓: 0.70 (1745 hom.)
• Consequence: LIPK NM_001080518.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

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]

KRT8P38 (HGNC:39872): (keratin 8 pseudogene 38)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIPK	NM_001080518.2	c.223+611A>G		intron_variant		ENST00000404190.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPK	ENST00000404190.3	c.223+611A>G		intron_variant		1	NM_001080518.2	P1
KRT8P38	ENST00000441370.1	n.39A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118010 AN: 151928 Hom.: 46827 Cov.: 31

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.783

GnomAD4 exome AF: 0.699 AC: 4824 AN: 6906 Hom.: 1745 Cov.: 0 AF XY: 0.698 AC XY: 2615 AN XY: 3744

Gnomad4 AFR exome AF: 0.931

Gnomad4 AMR exome AF: 0.827

Gnomad4 ASJ exome AF: 0.716

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.882

Gnomad4 FIN exome AF: 0.712

Gnomad4 NFE exome AF: 0.654

Gnomad4 OTH exome AF: 0.736

GnomAD4 genome AF: 0.777 AC: 118137 AN: 152046 Hom.: 46894 Cov.: 31 AF XY: 0.781 AC XY: 58016 AN XY: 74292

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.786

Alfa AF: 0.752 Hom.: 6227

Bravo AF: 0.792

Asia WGS AF: 0.921 AC: 3204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs412927; hg19: chr10-90487280;