rs150026164

Variant names:

• chr1-153261012-CGGCGGT-C
• rs150026164
• NM_000427.3:c.75_80delTGGCGG

Your query was ambiguous. Multiple possible variants found:

• chr1-153261012-CGGCGGT-C
• chr1-153261012-CGGCGGT-CGGCGGTGGCGGT
• chr1-153261012-CGGCGGT-CGGCGGTGGCGGTGGCGGTGGCGGCGGCGGTGGCGGT
• chr1-153261012-CGGCGGT-CGGCGGTGGCGGTGGCGGT
• chr1-153261012-CGGCGGT-CGGCGGTGGCGGTGGCGGTGGCGGT

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2 PM4 BP6

The NM_000427.3(LORICRIN):​c.75_80delTGGCGG​(p.Gly26_Gly27del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000281 in 1,421,080 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: LORICRIN NM_000427.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.68

Genes affected

LORICRIN (HGNC:6663): (loricrin cornified envelope precursor protein) This gene encodes loricrin, a major protein component of the cornified cell envelope found in terminally differentiated epidermal cells. Mutations in this gene are associated with Vohwinkel's syndrome and progressive symmetric erythrokeratoderma, both inherited skin diseases. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_000427.3.
• BP6: Variant 1-153261012-CGGCGGT-C is Benign according to our data. Variant chr1-153261012-CGGCGGT-C is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LORICRIN	NM_000427.3	c.75_80delTGGCGG	p.Gly26_Gly27del	disruptive_inframe_deletion	Exon 2 of 2	ENST00000368742.4	NP_000418.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LORICRIN	ENST00000368742.4	c.75_80delTGGCGG	p.Gly26_Gly27del	disruptive_inframe_deletion	Exon 2 of 2	1	NM_000427.3	ENSP00000357731.3

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome AF: 0.00000281 AC: 4 AN: 1421080 Hom.: 0 AF XY: 0.00000283 AC XY: 2 AN XY: 706498

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000243

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000274

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.17e-7

Gnomad4 OTH exome AF: 0.0000171

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

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: rs150026164; hg19: chr1-153233488;