rs7200240

Variant names:

• chr16-83138557-A-C
• rs7200240
• NM_001257.5:c.483+13056A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-83138557-A-C
• chr16-83138557-A-G
• chr16-83138557-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001257.5(CDH13):​c.483+13056A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,174 control chromosomes in the GnomAD database, including 3,764 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 0.21 (3764 hom., cov: 32)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH13	NM_001257.5	c.483+13056A>C		intron_variant	Intron 4 of 13	ENST00000567109.6	NP_001248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6	c.483+13056A>C		intron_variant	Intron 4 of 13	1	NM_001257.5	ENSP00000479395.1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32054 AN: 152056 Hom.: 3767 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.211 AC: 32063 AN: 152174 Hom.: 3764 Cov.: 32 AF XY: 0.212 AC XY: 15768 AN XY: 74388

African (AFR) AF: 0.120 AC: 4974 AN: 41538

American (AMR) AF: 0.172 AC: 2623 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3464

East Asian (EAS) AF: 0.174 AC: 900 AN: 5178

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4808

European-Finnish (FIN) AF: 0.331 AC: 3508 AN: 10592

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.259 AC: 17599 AN: 67996

Other (OTH) AF: 0.209 AC: 441 AN: 2114

Alfa AF: 0.194 Hom.: 1197

Bravo AF: 0.192

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.76
DANN	Benign	0.35
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7200240; hg19: chr16-83172162;