16-68730609-C-T

Position:

• chr16-68730609-C-T

Variant summary

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

The XM_047433450.1(CDH3):​c.*46-1460C>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 152,168 control chromosomes in the GnomAD database, including 50,154 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 (50154 hom., cov: 33)
• Consequence: CDH3 XM_047433450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

Genes affected

CDH3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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
CDH3	XM_047433450.1	c.*46-1460C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122557 AN: 152050 Hom.: 50147 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.806 AC: 122602 AN: 152168 Hom.: 50154 Cov.: 33 AF XY: 0.801 AC XY: 59596 AN XY: 74410

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.828

Alfa AF: 0.835 Hom.: 8318

Bravo AF: 0.797

Asia WGS AF: 0.774 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9989407; hg19: chr16-68764512;