rs7196661

Positions:

• chr16-68740009-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004360.5(CDH1):​c.163+1598C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,118 control chromosomes in the GnomAD database, including 50,112 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 0.81 (50112 hom., cov: 32)
• Consequence: CDH1 NM_004360.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH1	NM_004360.5	c.163+1598C>T		intron_variant		ENST00000261769.10
CDH1	NM_001317184.2	c.163+1598C>T		intron_variant
CDH1	NM_001317185.2	c.-1453+1598C>T		intron_variant
CDH1	NM_001317186.2	c.-1657+1598C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH1	ENST00000261769.10	c.163+1598C>T		intron_variant		1	NM_004360.5	P1
CDH1	ENST00000422392.6	c.163+1598C>T		intron_variant		1
CDH1	ENST00000566612.5	c.163+1598C>T		intron_variant, NMD_transcript_variant		1
CDH1	ENST00000566510.5	c.163+1598C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122488 AN: 152000 Hom.: 50106 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.806 AC: 122532 AN: 152118 Hom.: 50112 Cov.: 32 AF XY: 0.801 AC XY: 59544 AN XY: 74366

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.827

Alfa AF: 0.831 Hom.: 8987

Bravo AF: 0.797

Asia WGS AF: 0.774 AC: 2692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	16
DANN	Benign	0.86

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: rs7196661; hg19: chr16-68773912;