ENST00000565238.1:n.456A>C

Variant names:

• chr16-82954267-T-G
• rs11639621
• ENST00000565238.1:n.456A>C

Variant summary

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

The ENST00000565238.1(ENSG00000260832):​n.456A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,850 control chromosomes in the GnomAD database, including 24,721 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 0.55 (24713 hom., cov: 30)
  • Exomes 𝑓: 0.48 (8 hom.)
• Consequence: ENSG00000260832 ENST00000565238.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 4 publications found

Genes affected

ENSG00000260832 (HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565238.1. 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.158-77743T>G		intron	N/A	NP_001248.1
	LOC101928417	NR_110937.1		n.456A>C		non_coding_transcript_exon	Exon 3 of 3
	CDH13	NM_001220488.2		c.299-77743T>G		intron	N/A	NP_001207417.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260832	ENST00000565238.1	TSL:1	n.456A>C		non_coding_transcript_exon	Exon 3 of 3
	CDH13	ENST00000567109.6	TSL:1 MANE Select	c.158-77743T>G		intron	N/A	ENSP00000479395.1
	CDH13	ENST00000431540.7	TSL:1	c.158-77743T>G		intron	N/A	ENSP00000408632.3

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83786 AN: 151680 Hom.: 24690 Cov.: 30

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.583

GnomAD4 exome AF: 0.481 AC: 25 AN: 52 Hom.: 8 Cov.: 0 AF XY: 0.421 AC XY: 16 AN XY: 38

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.750 AC: 3 AN: 4

European-Non Finnish (NFE) AF: 0.452 AC: 19 AN: 42

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.552 AC: 83842 AN: 151798 Hom.: 24713 Cov.: 30 AF XY: 0.564 AC XY: 41847 AN XY: 74158

African (AFR) AF: 0.356 AC: 14732 AN: 41372

American (AMR) AF: 0.669 AC: 10201 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2101 AN: 3468

East Asian (EAS) AF: 0.914 AC: 4686 AN: 5128

South Asian (SAS) AF: 0.689 AC: 3291 AN: 4774

European-Finnish (FIN) AF: 0.659 AC: 6964 AN: 10568

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.590 AC: 40059 AN: 67930

Other (OTH) AF: 0.581 AC: 1224 AN: 2106

Alfa AF: 0.528 Hom.: 4602

Bravo AF: 0.547

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.41
PhyloP100		-0.053
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: rs11639621; hg19: chr16-82987872;