10-88761759-CTATG-C

Position:

• chr10-88761759-CTATG-C

Variant summary

Our verdict is Benign. Variant got -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

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 10-88761759-CTATG-C is Benign according to our data. Variant chr10-88761759-CTATG-C is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPN	NM_001102469.2	c.108+250_108+253delGTAT		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+247_108+250delTATG		intron_variant		1	NM_001102469.2	ENSP00000383923.1
LIPN	ENST00000674982.1	n.241+247_241+250delTATG		intron_variant

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

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0752

Gnomad4 NFE AF: 0.0957

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0628 Hom.: 1

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 21, 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: rs761121962; hg19: chr10-90521516;