chr10-88727619-A-T

Position:

• chr10-88727619-A-T

Variant summary

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

The NM_001080518.2(LIPK):​c.223+707A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 160,938 control chromosomes in the GnomAD database, including 49,026 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 (46753 hom., cov: 30)
  • Exomes 𝑓: 0.70 (2273 hom.)
• Consequence: LIPK NM_001080518.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849

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=-1.0).
• 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+707A>T		intron_variant		ENST00000404190.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPK	ENST00000404190.3	c.223+707A>T		intron_variant		1	NM_001080518.2	P1
KRT8P38	ENST00000441370.1	n.135A>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117740 AN: 151680 Hom.: 46685 Cov.: 30

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.783

GnomAD4 exome AF: 0.697 AC: 6371 AN: 9138 Hom.: 2273 Cov.: 0 AF XY: 0.706 AC XY: 3488 AN XY: 4944

Gnomad4 AFR exome AF: 0.900

Gnomad4 AMR exome AF: 0.838

Gnomad4 ASJ exome AF: 0.811

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.796

Gnomad4 FIN exome AF: 0.702

Gnomad4 NFE exome AF: 0.658

Gnomad4 OTH exome AF: 0.736

GnomAD4 genome AF: 0.776 AC: 117869 AN: 151800 Hom.: 46753 Cov.: 30 AF XY: 0.780 AC XY: 57878 AN XY: 74170

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.785

Alfa AF: 0.635 Hom.: 1997

Bravo AF: 0.792

Asia WGS AF: 0.921 AC: 3202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.48

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: rs390414; hg19: chr10-90487376;