16-82902438-A-G

Position:

• chr16-82902438-A-G

Variant summary

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

The NM_001257.5(CDH13):​c.157+43965A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,008 control chromosomes in the GnomAD database, including 65,986 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 0.93 (65986 hom., cov: 29)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35

Genes affected

CDH13 (HGNC:1753): (cadherin 13) This gene encodes a member of the cadherin superfamily. The encoded protein is localized to the surface of the cell membrane and is anchored by a GPI moiety, rather than by a transmembrane domain. The protein lacks the cytoplasmic domain characteristic of other cadherins, and so is not thought to be a cell-cell adhesion glycoprotein. This protein acts as a negative regulator of axon growth during neural differentiation. It also protects vascular endothelial cells from apoptosis due to oxidative stress, and is associated with resistance to atherosclerosis. The gene is hypermethylated in many types of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2011]

LOC124903733 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH13	NM_001257.5	c.157+43965A>G		intron_variant		ENST00000567109.6	NP_001248.1
LOC124903733	XR_007065146.1	n.5447A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6	c.157+43965A>G		intron_variant		1	NM_001257.5	ENSP00000479395	P1

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141382 AN: 151890 Hom.: 65928 Cov.: 29

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.931 AC: 141501 AN: 152008 Hom.: 65986 Cov.: 29 AF XY: 0.926 AC XY: 68775 AN XY: 74278

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.939

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.834

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.929

Alfa AF: 0.924 Hom.: 26117

Bravo AF: 0.942

Asia WGS AF: 0.871 AC: 3030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	20
DANN	Benign	0.79

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: rs9319578; hg19: chr16-82936043;