rs9935563

chr16-68827753-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004360.5(CDH1):c.2165-421T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 151,696 control chromosomes in the GnomAD database, including 38,226 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (38226 hom., cov: 29)
• Consequence: CDH1 NM_004360.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH1	NM_004360.5	c.2165-421T>C		intron_variant		ENST00000261769.10
CDH1	NM_001317184.2	c.1982-421T>C		intron_variant
CDH1	NM_001317185.2	c.617-421T>C		intron_variant
CDH1	NM_001317186.2	c.200-421T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH1	ENST00000261769.10	c.2165-421T>C		intron_variant		1	NM_004360.5	P1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106200 AN: 151576 Hom.: 38165 Cov.: 29

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.701 AC: 106327 AN: 151696 Hom.: 38226 Cov.: 29 AF XY: 0.698 AC XY: 51718 AN XY: 74048

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.688

Alfa AF: 0.651 Hom.: 7691

Bravo AF: 0.712

Asia WGS AF: 0.714 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.90
Dann	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs9935563; hg19: chr16-68861656;