16-68737515-C-CGCCCCAGCCCCGTGCCCCAGCCCTGCGCCCCAGCCCCGT

Position:

• chr16-68737515-C-CGCCCCAGCCCCGTGCCCCAGCCCTGCGCCCCAGCCCCGT

Variant summary

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

The NM_004360.5(CDH1):​c.48+62_48+63insCGTGCCCCAGCCCTGCGCCCCAGCCCCGTGCCCCAGCCC 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: 𝑓 0.0000068 (0 hom., cov: 0)
• 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	Protein	UniProt
CDH1	NM_004360.5	c.48+62_48+63insCGTGCCCCAGCCCTGCGCCCCAGCCCCGTGCCCCAGCCC		intron_variant		ENST00000261769.10	NP_004351.1
CDH1	NM_001317184.2	c.48+62_48+63insCGTGCCCCAGCCCTGCGCCCCAGCCCCGTGCCCCAGCCC		intron_variant			NP_001304113.1
CDH1	NM_001317185.2	c.-1568+62_-1568+63insCGTGCCCCAGCCCTGCGCCCCAGCCCCGTGCCCCAGCCC		intron_variant			NP_001304114.1
CDH1	NM_001317186.2	c.-1772+62_-1772+63insCGTGCCCCAGCCCTGCGCCCCAGCCCCGTGCCCCAGCCC		intron_variant			NP_001304115.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH1	ENST00000261769.10	c.48+62_48+63insCGTGCCCCAGCCCTGCGCCCCAGCCCCGTGCCCCAGCCC		intron_variant		1	NM_004360.5	ENSP00000261769.4
CDH1	ENST00000422392.6	c.48+62_48+63insCGTGCCCCAGCCCTGCGCCCCAGCCCCGTGCCCCAGCCC		intron_variant		1		ENSP00000414946.2
CDH1	ENST00000566612.5	n.48+62_48+63insCGTGCCCCAGCCCTGCGCCCCAGCCCCGTGCCCCAGCCC		intron_variant		1		ENSP00000454782.1
CDH1	ENST00000566510.5	n.48+62_48+63insCGTGCCCCAGCCCTGCGCCCCAGCCCCGTGCCCCAGCCC		intron_variant		5		ENSP00000458139.1

Frequencies

GnomAD3 genomes AF: 0.00000677 AC: 1 AN: 147816 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000677 AC: 1 AN: 147816 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 72246

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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: rs45625236; hg19: chr16-68771418;