chr10-88761718-GCTATCTATCTAT-G

Variant names:

• chr10-88761718-GCTATCTATCTAT-G
• rs71022539
• NM_001102469.2:c.108+238_108+249delCTATCTATCTAT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001102469.2(LIPN):​c.108+238_108+249delCTATCTATCTAT 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. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (1402 hom., cov: 0)
• Consequence: LIPN NM_001102469.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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: Benign. The variant received -10 ACMG points.

• BP6: Variant 10-88761718-GCTATCTATCTAT-G is Benign according to our data. Variant chr10-88761718-GCTATCTATCTAT-G is described in ClinVar as Benign. ClinVar VariationId is 1242496.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

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+238_108+249delCTATCTATCTAT		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+217delCTATCTATCTAT		intron	N/A	ENSP00000383923.1	Q5VXI9
	LIPN	ENST00000674982.1		n.241+206_241+217delCTATCTATCTAT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 19318 AN: 145682 Hom.: 1400 Cov.: 0

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.133 AC: 19341 AN: 145802 Hom.: 1402 Cov.: 0 AF XY: 0.132 AC XY: 9383 AN XY: 70894

African (AFR) AF: 0.191 AC: 7504 AN: 39372

American (AMR) AF: 0.0926 AC: 1328 AN: 14340

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 460 AN: 3376

East Asian (EAS) AF: 0.0627 AC: 311 AN: 4960

South Asian (SAS) AF: 0.200 AC: 915 AN: 4570

European-Finnish (FIN) AF: 0.111 AC: 1094 AN: 9862

Middle Eastern (MID) AF: 0.136 AC: 39 AN: 286

European-Non Finnish (NFE) AF: 0.108 AC: 7172 AN: 66174

Other (OTH) AF: 0.138 AC: 275 AN: 2000

Alfa AF: 0.0650 Hom.: 63

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

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

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;