rs11642413

chr16-68756491-G-A

Variant summary

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

The NM_004360.5(CDH1):c.163+18080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,624 control chromosomes in the GnomAD database, including 19,650 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 0.49 (19650 hom., cov: 30)
• Consequence: CDH1 NM_004360.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH1	NM_004360.5	c.163+18080G>A		intron_variant		ENST00000261769.10
CDH1	NM_001317184.2	c.163+18080G>A		intron_variant
CDH1	NM_001317185.2	c.-1453+18080G>A		intron_variant
CDH1	NM_001317186.2	c.-1657+18080G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH1	ENST00000261769.10	c.163+18080G>A		intron_variant		1	NM_004360.5	P1
CDH1	ENST00000422392.6	c.163+18080G>A		intron_variant		1
CDH1	ENST00000566612.5	c.163+18080G>A		intron_variant, NMD_transcript_variant		1
CDH1	ENST00000566510.5	c.163+18080G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74850 AN: 151506 Hom.: 19647 Cov.: 30

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.494 AC: 74869 AN: 151624 Hom.: 19650 Cov.: 30 AF XY: 0.493 AC XY: 36464 AN XY: 74032

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.510

Alfa AF: 0.561 Hom.: 21457

Bravo AF: 0.476

Asia WGS AF: 0.473 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.030
Dann	Benign	0.81

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: rs11642413; hg19: chr16-68790394;