10-88761755-CTATCTATG-C

Variant names:

• chr10-88761755-CTATCTATG-C
• rs200398534
• NM_001102469.2:c.108+250_108+257delGTATCTAT

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+250_108+257delGTATCTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (483 hom., cov: 0)
• Consequence: LIPN NM_001102469.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.04
• 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 10-88761755-CTATCTATG-C is Benign according to our data. Variant chr10-88761755-CTATCTATG-C is described in ClinVar as Benign. ClinVar VariationId is 1242906.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 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+250_108+257delGTATCTAT		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+243_108+250delTATCTATG		intron	N/A	ENSP00000383923.1	Q5VXI9
	LIPN	ENST00000674982.1		n.241+243_241+250delTATCTATG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 11497 AN: 97206 Hom.: 479 Cov.: 0

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0915

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.0835

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0803

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.118 AC: 11509 AN: 97240 Hom.: 483 Cov.: 0 AF XY: 0.121 AC XY: 5660 AN XY: 46908

African (AFR) AF: 0.136 AC: 2454 AN: 17986

American (AMR) AF: 0.193 AC: 1863 AN: 9662

Ashkenazi Jewish (ASJ) AF: 0.0835 AC: 203 AN: 2432

East Asian (EAS) AF: 0.228 AC: 498 AN: 2180

South Asian (SAS) AF: 0.160 AC: 465 AN: 2912

European-Finnish (FIN) AF: 0.0803 AC: 579 AN: 7210

Middle Eastern (MID) AF: 0.0990 AC: 19 AN: 192

European-Non Finnish (NFE) AF: 0.0986 AC: 5191 AN: 52644

Other (OTH) AF: 0.132 AC: 170 AN: 1290

Alfa AF: 0.0718 Hom.: 0

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		1.0
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: rs200398534; hg19: chr10-90521512;