rs9332462

Variant names:

• chr16-83284124-G-A
• rs9332462
• NM_001257.5:c.637-60738G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-83284124-G-A
• chr16-83284124-G-C
• chr16-83284124-G-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.637-60738G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,908 control chromosomes in the GnomAD database, including 14,209 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 0.42 (14209 hom., cov: 32)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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 (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH13	NM_001257.5	c.637-60738G>A		intron_variant	Intron 5 of 13	ENST00000567109.6	NP_001248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6	c.637-60738G>A		intron_variant	Intron 5 of 13	1	NM_001257.5	ENSP00000479395.1

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64219 AN: 151790 Hom.: 14211 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.423 AC: 64234 AN: 151908 Hom.: 14209 Cov.: 32 AF XY: 0.428 AC XY: 31734 AN XY: 74222

African (AFR) AF: 0.296 AC: 12266 AN: 41412

American (AMR) AF: 0.525 AC: 8005 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1643 AN: 3470

East Asian (EAS) AF: 0.647 AC: 3333 AN: 5148

South Asian (SAS) AF: 0.573 AC: 2757 AN: 4808

European-Finnish (FIN) AF: 0.431 AC: 4553 AN: 10552

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30176 AN: 67946

Other (OTH) AF: 0.434 AC: 917 AN: 2112

Alfa AF: 0.440 Hom.: 61688

Bravo AF: 0.422

Asia WGS AF: 0.574 AC: 1995 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.38
PhyloP100		-0.016
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

Publications

Loading publications...

Other links and lift over

dbSNP: rs9332462; hg19: chr16-83317729;