10-88761718-GCTATCTATCTATCTATCTATCTAT-GCTATCTAT

Variant names:

• chr10-88761718-GCTATCTATCTATCTAT-G
• rs71022539
• NM_001102469.2:c.108+234_108+249delCTATCTATCTATCTAT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001102469.2(LIPN):​c.108+234_108+249delCTATCTATCTATCTAT 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 0.0093 (12 hom., cov: 0)
• Consequence: LIPN NM_001102469.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 0 publications found

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 12 AR,Unknown gene

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.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPN	NM_001102469.2	MANE Select	c.108+234_108+249delCTATCTATCTATCTAT		intron	N/A	NP_001095939.1	Q5VXI9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPN	ENST00000404459.2	TSL:1 MANE Select	c.108+206_108+221delCTATCTATCTATCTAT		intron	N/A	ENSP00000383923.1	Q5VXI9
	LIPN	ENST00000674982.1		n.241+206_241+221delCTATCTATCTATCTAT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00929 AC: 1354 AN: 145746 Hom.: 12 Cov.: 0

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00831

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.000201

Gnomad SAS AF: 0.00197

Gnomad FIN AF: 0.000507

Gnomad MID AF: 0.0387

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.0126

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00928 AC: 1354 AN: 145866 Hom.: 12 Cov.: 0 AF XY: 0.00885 AC XY: 628 AN XY: 70934

African (AFR) AF: 0.0115 AC: 453 AN: 39404

American (AMR) AF: 0.00823 AC: 118 AN: 14346

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 46 AN: 3376

East Asian (EAS) AF: 0.000202 AC: 1 AN: 4960

South Asian (SAS) AF: 0.00197 AC: 9 AN: 4572

European-Finnish (FIN) AF: 0.000507 AC: 5 AN: 9868

Middle Eastern (MID) AF: 0.0417 AC: 12 AN: 288

European-Non Finnish (NFE) AF: 0.0103 AC: 684 AN: 66190

Other (OTH) AF: 0.0130 AC: 26 AN: 2000

Alfa AF: 0.00224 Hom.: 63

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.43
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs71022539; hg19: chr10-90521475;