Variant 10-88761763-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001102469.2(LIPN):c.108+250G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 183 hom., cov: 0)

Consequence

LIPN
NM_001102469.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.42

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.14).

BP6

Variant 10-88761763-G-C is Benign according to our data. Variant chr10-88761763-G-C is described in ClinVar as [Benign]. Clinvar id is 1220835.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPN	NM_001102469.2 link	c.108+250G>C		intron_variant		ENST00000404459.2	NP_001095939.1	Q5VXI9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPN	ENST00000404459.2 link	c.108+250G>C		intron_variant		1	NM_001102469.2	ENSP00000383923.1		Q5VXI9
LIPN	ENST00000674982.1 link	n.241+250G>C		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

6837

AN:

50846

Hom.:

186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.0583

Gnomad MID

AF:

0.178

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.123

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

GnomAD4 genome

AF:

0.134

AC:

6838

AN:

50856

Hom.:

183

Cov.:

AF XY:

0.132

AC XY:

3215

AN XY:

24306

show subpopulations

Gnomad4 AFR

AF:

0.214

Gnomad4 AMR

AF:

0.123

Gnomad4 ASJ

AF:

0.125

Gnomad4 EAS

AF:

0.249

Gnomad4 SAS

AF:

0.168

Gnomad4 FIN

AF:

0.0583

Gnomad4 NFE

AF:

0.108

Gnomad4 OTH

AF:

0.122

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

1.0

DANN

Benign

0.12

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over