10-88765567-T-C

Position:

• chr10-88765567-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001102469.2(LIPN):​c.426-702T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,796 control chromosomes in the GnomAD database, including 4,213 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4213 hom., cov: 32)
• Consequence: LIPN NM_001102469.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPN	NM_001102469.2	c.426-702T>C		intron_variant		ENST00000404459.2	NP_001095939.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPN	ENST00000404459.2	c.426-702T>C		intron_variant		1	NM_001102469.2	ENSP00000383923.1
LIPN	ENST00000674982.1	n.1517T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35205 AN: 151678 Hom.: 4200 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.232 AC: 35254 AN: 151796 Hom.: 4213 Cov.: 32 AF XY: 0.231 AC XY: 17169 AN XY: 74170

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.218

Alfa AF: 0.231 Hom.: 685

Bravo AF: 0.240

Asia WGS AF: 0.290 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.68

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: rs366107; hg19: chr10-90525324;