10-88727619-A-T

Variant names:

• chr10-88727619-A-T
• rs390414
• NM_001080518.2:c.223+707A>T

Variant summary

Our verdict is Benign. The variant received -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
• 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]

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LIPK	NM_001080518.2	c.223+707A>T		intron_variant	Intron 3 of 9	ENST00000404190.3	NP_001073987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPK	ENST00000404190.3	c.223+707A>T		intron_variant	Intron 3 of 9	1	NM_001080518.2	ENSP00000383900.1
KRT8P38	ENST00000441370.1	n.135A>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.900 AC: 90 AN: 100

American (AMR) AF: 0.838 AC: 402 AN: 480

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 133 AN: 164

East Asian (EAS) AF: 1.00 AC: 150 AN: 150

South Asian (SAS) AF: 0.796 AC: 535 AN: 672

European-Finnish (FIN) AF: 0.702 AC: 514 AN: 732

Middle Eastern (MID) AF: 0.769 AC: 20 AN: 26

European-Non Finnish (NFE) AF: 0.658 AC: 4091 AN: 6222

Other (OTH) AF: 0.736 AC: 436 AN: 592

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

African (AFR) AF: 0.931 AC: 38549 AN: 41408

American (AMR) AF: 0.801 AC: 12230 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2652 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5151 AN: 5172

South Asian (SAS) AF: 0.820 AC: 3943 AN: 4808

European-Finnish (FIN) AF: 0.708 AC: 7429 AN: 10494

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45250 AN: 67864

Other (OTH) AF: 0.785 AC: 1657 AN: 2110

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
PhyloP100		-0.85
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: rs390414; hg19: chr10-90487376;