rs45625236

chr16-68737515-C-CGCCCCAGCCCCGGchr16-68737515-C-CGCCCCAGCCCCGTchr16-68737515-C-CGCCCCAGCCCCGTGCCCCAGCCCTGCGCCCCAGCCCCGTchr16-68737515-C-CGCCCCAGCCCCTTchr16-68737515-C-CGCCCCAGCCCGGT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_004360.5(CDH1):c.48+62_48+63insCGGGCCCCAGCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CDH1 NM_004360.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

Genes affected

CDH1 (HGNC:1748): (cadherin 1) This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Mutations in this gene are correlated with gastric, breast, colorectal, thyroid and ovarian cancer. Loss of function of this gene is thought to contribute to cancer progression by increasing proliferation, invasion, and/or metastasis. The ectodomain of this protein mediates bacterial adhesion to mammalian cells and the cytoplasmic domain is required for internalization. This gene is present in a gene cluster with other members of the cadherin family on chromosome 16. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH1	NM_004360.5	c.48+62_48+63insCGGGCCCCAGCCC		intron_variant		ENST00000261769.10
CDH1	NM_001317184.2	c.48+62_48+63insCGGGCCCCAGCCC		intron_variant
CDH1	NM_001317185.2	c.-1568+62_-1568+63insCGGGCCCCAGCCC		intron_variant
CDH1	NM_001317186.2	c.-1772+62_-1772+63insCGGGCCCCAGCCC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH1	ENST00000261769.10	c.48+62_48+63insCGGGCCCCAGCCC		intron_variant		1	NM_004360.5	P1
CDH1	ENST00000422392.6	c.48+62_48+63insCGGGCCCCAGCCC		intron_variant		1
CDH1	ENST00000566612.5	c.48+62_48+63insCGGGCCCCAGCCC		intron_variant, NMD_transcript_variant		1
CDH1	ENST00000566510.5	c.48+62_48+63insCGGGCCCCAGCCC		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1203558 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 602240

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-68771418;