10-88761759-CTATG-C

Variant names:

• chr10-88761759-CTATG-C
• rs761121962
• NM_001102469.2:c.108+250_108+253delGTAT

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+253delGTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (271 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 10-88761759-CTATG-C is Benign according to our data. Variant chr10-88761759-CTATG-C is described in ClinVar as Benign. ClinVar VariationId is 1264290.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 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+253delGTAT		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+247_108+250delTATG		intron	N/A	ENSP00000383923.1	Q5VXI9
	LIPN	ENST00000674982.1		n.241+247_241+250delTATG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 9249 AN: 87022 Hom.: 271 Cov.: 0

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0422

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.0928

Gnomad NFE AF: 0.0957

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.106 AC: 9258 AN: 87064 Hom.: 271 Cov.: 0 AF XY: 0.107 AC XY: 4488 AN XY: 42074

African (AFR) AF: 0.120 AC: 1925 AN: 16088

American (AMR) AF: 0.114 AC: 887 AN: 7768

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 392 AN: 2406

East Asian (EAS) AF: 0.190 AC: 441 AN: 2326

South Asian (SAS) AF: 0.159 AC: 421 AN: 2640

European-Finnish (FIN) AF: 0.0752 AC: 505 AN: 6714

Middle Eastern (MID) AF: 0.0968 AC: 18 AN: 186

European-Non Finnish (NFE) AF: 0.0957 AC: 4515 AN: 47172

Other (OTH) AF: 0.111 AC: 128 AN: 1148

Alfa AF: 0.0628 Hom.: 1

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

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs761121962; hg19: chr10-90521516;