GeneBe

rs71022539

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001102469.2(LIPN):​c.108+226_108+249delCTATCTATCTATCTATCTATCTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)

Consequence

LIPN
NM_001102469.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.429

Publications

0 publications found
Variant links:
Genes affected
LIPN (HGNC:23452): (lipase family member N) The gene encodes a lipase that is highly expressed in granular keratinocytes in the epidermis, and plays a role in the differentiation of keratinocytes. Mutations in this gene are associated with lamellar ichthyosis type 4. [provided by RefSeq, Dec 2011]
LIPN Gene-Disease associations (from GenCC):
  • autosomal recessive congenital ichthyosis 8
    Inheritance: Unknown, AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P
  • lamellar ichthyosis
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102469.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
LIPN
NM_001102469.2
MANE Select
c.108+226_108+249delCTATCTATCTATCTATCTATCTAT
intron
N/ANP_001095939.1Q5VXI9

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
LIPN
ENST00000404459.2
TSL:1 MANE Select
c.108+206_108+229delCTATCTATCTATCTATCTATCTAT
intron
N/AENSP00000383923.1Q5VXI9
LIPN
ENST00000674982.1
n.241+206_241+229delCTATCTATCTATCTATCTATCTAT
intron
N/A

Frequencies

GnomAD3 genomes
AF:
0.0000137
AC:
2
AN:
145754
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000255
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000151
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000137
AC:
2
AN:
145874
Hom.:
0
Cov.:
0
AF XY:
0.0000141
AC XY:
1
AN XY:
70938
show subpopulations
African (AFR)
AF:
0.0000254
AC:
1
AN:
39410
American (AMR)
AF:
0.00
AC:
0
AN:
14346
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3376
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4960
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4572
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9868
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
288
European-Non Finnish (NFE)
AF:
0.0000151
AC:
1
AN:
66192
Other (OTH)
AF:
0.00
AC:
0
AN:
2000
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
63

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.43

Splicing

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

Publications

Other links and lift over

dbSNP: rs71022539; hg19: chr10-90521475; API