Genetic Variant LUM:c.-152_-151insCC (chr12-91111527-A-AGG) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_002345.4(LUM):c.-152_-151insCC variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.88 ( 58033 hom., cov: 0)

Exomes 𝑓: 0.92 ( 15 hom. )

Consequence

LUM
NM_002345.4 upstream_gene

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.360

Publications

3 publications found

Variant links:

Genes affected

LUM (HGNC:6724): (lumican) This gene encodes a member of the small leucine-rich proteoglycan (SLRP) family that includes decorin, biglycan, fibromodulin, keratocan, epiphycan, and osteoglycin. In these bifunctional molecules, the protein moiety binds collagen fibrils and the highly charged hydrophilic glycosaminoglycans regulate interfibrillar spacings. Lumican is the major keratan sulfate proteoglycan of the cornea but is also distributed in interstitial collagenous matrices throughout the body. Lumican may regulate collagen fibril organization and circumferential growth, corneal transparency, and epithelial cell migration and tissue repair. [provided by RefSeq, Jul 2008]

LUM links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_002345.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002345.4. 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
	LUM	NM_002345.4	MANE Select	c.-152_-151insCC		upstream_gene	N/A	NP_002336.1	P51884

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LUM	ENST00000266718.5	TSL:1 MANE Select	c.-152_-151insCC	upstream_gene	N/A	ENSP00000266718.4	P51884
LUM	ENST00000891369.1		c.-239_-238insCC	upstream_gene	N/A	ENSP00000561428.1
LUM	ENST00000963638.1		c.-147_-146insCC	upstream_gene	N/A	ENSP00000633697.1

Frequencies

GnomAD3 genomes

AF:

0.883

AC:

131252

AN:

148596

Hom.:

58013

Cov.:

show subpopulations

Gnomad AFR

AF:

0.795

Gnomad AMI

AF:

0.810

Gnomad AMR

AF:

0.857

Gnomad ASJ

AF:

0.952

Gnomad EAS

AF:

0.733

Gnomad SAS

AF:

0.882

Gnomad FIN

AF:

0.953

Gnomad MID

AF:

0.867

Gnomad NFE

AF:

0.939

Gnomad OTH

AF:

0.885

GnomAD4 exome

AF:

0.917

AC:

AN:

Hom.:

Cov.:

AF XY:

0.923

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.906

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.642

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.883

AC:

131317

AN:

148704

Hom.:

58033

Cov.:

AF XY:

0.881

AC XY:

63914

AN XY:

72518

show subpopulations

African (AFR)

AF:

0.794

AC:

31318

AN:

39438

American (AMR)

AF:

0.857

AC:

12820

AN:

14956

Ashkenazi Jewish (ASJ)

AF:

0.952

AC:

3280

AN:

3444

East Asian (EAS)

AF:

0.733

AC:

3689

AN:

5030

South Asian (SAS)

AF:

0.882

AC:

4175

AN:

4736

European-Finnish (FIN)

AF:

0.953

AC:

9741

AN:

10224

Middle Eastern (MID)

AF:

0.874

AC:

257

AN:

294

European-Non Finnish (NFE)

AF:

0.939

AC:

63474

AN:

67610

Other (OTH)

AF:

0.885

AC:

1834

AN:

2072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

610

1221

1831

2442

3052

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

886

1772

2658

3544

4430

<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:

0.906

Hom.:

1974

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.36

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over