10-88761718-GCTAT-G

Position:

• chr10-88761718-GCTAT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001102469.2(LIPN):​c.108+246_108+249delCTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.081 (532 hom., cov: 0)
• Consequence: LIPN NM_001102469.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.429

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-88761718-GCTAT-G is Benign according to our data. Variant chr10-88761718-GCTAT-G is described in ClinVar as [Benign]. Clinvar id is 1246521.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPN	NM_001102469.2	c.108+246_108+249delCTAT		intron_variant		ENST00000404459.2	NP_001095939.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPN	ENST00000404459.2	c.108+206_108+209delCTAT		intron_variant		1	NM_001102469.2	ENSP00000383923.1
LIPN	ENST00000674982.1	n.241+206_241+209delCTAT		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0815 AC: 11867 AN: 145688 Hom.: 530 Cov.: 0

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.0708

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0938

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0815 AC: 11881 AN: 145806 Hom.: 532 Cov.: 0 AF XY: 0.0813 AC XY: 5765 AN XY: 70906

Gnomad4 AFR AF: 0.0553

Gnomad4 AMR AF: 0.0870

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0869

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0673

Gnomad4 NFE AF: 0.0939

Gnomad4 OTH AF: 0.0924

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs71022539; hg19: chr10-90521475;