NM_001257.5:c.157+33471G>T

Variant names:

• chr16-82891944-G-T
• rs16958826
• NM_001257.5:c.157+33471G>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.157+33471G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,110 control chromosomes in the GnomAD database, including 3,008 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 0.20 (3008 hom., cov: 32)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849
• Publications: 9 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 = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001257.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH13	NM_001257.5	MANE Select	c.157+33471G>T		intron	N/A	NP_001248.1
	CDH13	NM_001220488.2		c.298+33471G>T		intron	N/A	NP_001207417.1
	CDH13	NM_001220489.2		c.157+33471G>T		intron	N/A	NP_001207418.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH13	ENST00000567109.6	TSL:1 MANE Select	c.157+33471G>T		intron	N/A	ENSP00000479395.1
	CDH13	ENST00000431540.7	TSL:1	c.157+33471G>T		intron	N/A	ENSP00000408632.3
	CDH13	ENST00000268613.14	TSL:2	c.298+33471G>T		intron	N/A	ENSP00000268613.10

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30023 AN: 151992 Hom.: 3005 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0722

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.197 AC: 30036 AN: 152110 Hom.: 3008 Cov.: 32 AF XY: 0.197 AC XY: 14649 AN XY: 74376

African (AFR) AF: 0.192 AC: 7957 AN: 41522

American (AMR) AF: 0.193 AC: 2950 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3470

East Asian (EAS) AF: 0.0726 AC: 372 AN: 5124

South Asian (SAS) AF: 0.146 AC: 702 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10588

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14024 AN: 67984

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.201 Hom.: 5436

Bravo AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.43
PhyloP100		-0.85
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: rs16958826; hg19: chr16-82925549;