Genetic Variant LIPK:c.223+1050T>G (chr10-88727962-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080518.2(LIPK):c.223+1050T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 340,590 control chromosomes in the GnomAD database, including 97,059 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 0.77 ( 45636 hom., cov: 31)

Exomes 𝑓: 0.73 ( 51423 hom. )

Consequence

LIPK
NM_001080518.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.469

Publications

2 publications found

Variant links:

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]

LIPK links:

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

KRT8P38 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPK	NM_001080518.2	MANE Select	c.223+1050T>G		intron	N/A	NP_001073987.1	Q5VXJ0
	LIPK	NM_001378091.1		c.223+1050T>G		intron	N/A	NP_001365020.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPK	ENST00000404190.3	TSL:1 MANE Select	c.223+1050T>G		intron	N/A	ENSP00000383900.1	Q5VXJ0
	KRT8P38	ENST00000441370.1	TSL:6	n.478T>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.768

AC:

116674

AN:

151992

Hom.:

45576

Cov.:

show subpopulations

Gnomad AFR

AF:

0.901

Gnomad AMI

AF:

0.852

Gnomad AMR

AF:

0.795

Gnomad ASJ

AF:

0.753

Gnomad EAS

AF:

0.996

Gnomad SAS

AF:

0.819

Gnomad FIN

AF:

0.709

Gnomad MID

AF:

0.804

Gnomad NFE

AF:

0.667

Gnomad OTH

AF:

0.777

GnomAD4 exome

AF:

0.731

AC:

137772

AN:

188480

Hom.:

51423

Cov.:

AF XY:

0.732

AC XY:

79972

AN XY:

109192

show subpopulations

African (AFR)

AF:

0.906

AC:

4398

AN:

4856

American (AMR)

AF:

0.855

AC:

15032

AN:

17590

Ashkenazi Jewish (ASJ)

AF:

0.752

AC:

2673

AN:

3556

East Asian (EAS)

AF:

0.999

AC:

8282

AN:

8292

South Asian (SAS)

AF:

0.802

AC:

25189

AN:

31396

European-Finnish (FIN)

AF:

0.713

AC:

7532

AN:

10570

Middle Eastern (MID)

AF:

0.755

AC:

441

AN:

584

European-Non Finnish (NFE)

AF:

0.660

AC:

68037

AN:

103026

Other (OTH)

AF:

0.719

AC:

6188

AN:

8610

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1653

3307

4960

6614

8267

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

624

1248

1872

2496

3120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.768

AC:

116793

AN:

152110

Hom.:

45636

Cov.:

AF XY:

0.772

AC XY:

57405

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.901

AC:

37428

AN:

41532

American (AMR)

AF:

0.796

AC:

12160

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.753

AC:

2612

AN:

3470

East Asian (EAS)

AF:

0.996

AC:

5165

AN:

5184

South Asian (SAS)

AF:

0.820

AC:

3946

AN:

4814

European-Finnish (FIN)

AF:

0.709

AC:

7488

AN:

10562

Middle Eastern (MID)

AF:

0.803

AC:

236

AN:

294

European-Non Finnish (NFE)

AF:

0.667

AC:

45339

AN:

67954

Other (OTH)

AF:

0.779

AC:

1642

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1310

2621

3931

5242

6552

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.681

Hom.:

3861

Bravo

AF:

0.782

Asia WGS

AF:

0.920

AC:

3199

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

4.9

(source)

DANN

Benign

0.62

PhyloP100

0.47

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over