ENST00000621372.4:c.69dupC

Variant names:

• chr19-35248945-T-TC
• rs368776746
• ENST00000621372.4:c.69dupC

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000621372.4(LSR):​c.69dupC​(p.Trp24LeufsTer57) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: LSR ENST00000621372.4 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 0 publications found

Genes affected

LSR (HGNC:29572): (lipolysis stimulated lipoprotein receptor) Predicted to be involved in several processes, including establishment of skin barrier; protein localization to tricellular tight junction; and tricellular tight junction assembly. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000621372.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSR	NM_205834.4	MANE Select	c.-78_-77insC		upstream_gene	N/A	NP_991403.2	S4R3V8
	LSR	NM_015925.7		c.-78_-77insC		upstream_gene	N/A	NP_057009.4
	LSR	NM_001260489.2		c.-78_-77insC		upstream_gene	N/A	NP_001247418.2	A0A8Z5DL71

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSR	ENST00000621372.4	TSL:1	c.69dupC	p.Trp24LeufsTer57	frameshift	Exon 1 of 10	ENSP00000480821.1	Q86X29-1
	LSR	ENST00000347609.8	TSL:1	c.69dupC	p.Trp24LeufsTer105	frameshift	Exon 1 of 9	ENSP00000262627.3	Q86X29-2
	LSR	ENST00000361790.7	TSL:1	c.-76dupC		5_prime_UTR	Exon 1 of 10	ENSP00000354575.3	S4R3V8

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.17

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

Other links and lift over

dbSNP: rs368776746; hg19: chr19-35739848;