10-88761718-G-GCTAT

Variant names:

• chr10-88761718-G-GCTAT
• rs71022539
• NM_001102469.2:c.108+246_108+249dupCTAT

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+249dupCTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (1450 hom., cov: 0)
• Consequence: LIPN NM_001102469.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.694

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-G-GCTAT is Benign according to our data. Variant chr10-88761718-G-GCTAT is described in ClinVar as [Benign]. Clinvar id is 1228278.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPN	NM_001102469.2	c.108+246_108+249dupCTAT		intron_variant	Intron 2 of 9	ENST00000404459.2	NP_001095939.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPN	ENST00000404459.2	c.108+205_108+206insCTAT		intron_variant	Intron 2 of 9	1	NM_001102469.2	ENSP00000383923.1
LIPN	ENST00000674982.1	n.241+205_241+206insCTAT		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 18748 AN: 145638 Hom.: 1448 Cov.: 0

Gnomad AFR AF: 0.0777

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.0795

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0742

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.129 AC: 18750 AN: 145758 Hom.: 1450 Cov.: 0 AF XY: 0.127 AC XY: 8987 AN XY: 70888

Gnomad4 AFR AF: 0.0775

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.0194

Gnomad4 SAS AF: 0.0790

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.117

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 21, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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;