16-83748390-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001257.5(CDH13):​c.1681+140A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0394 in 720,782 control chromosomes in the GnomAD database, including 750 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.033 ( 126 hom., cov: 32)
Exomes 𝑓: 0.041 ( 624 hom. )

Consequence

CDH13
NM_001257.5 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0290
Variant links:
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]
CEDORA (HGNC:56653): (CDH13 antisense oligodendrocyte and neuron associated lncRNA)
HSBP1 (HGNC:5203): (heat shock factor binding protein 1) The heat-shock response is elicited by exposure of cells to thermal and chemical stress and through the activation of HSFs (heat shock factors) results in the elevated expression of heat-shock induced genes. Heat shock factor binding protein 1 (HSBP1), is a 76-amino-acid protein that binds to heat shock factor 1(HSF1), which is a transcription factor involved in the HS response. During HS response, HSF1 undergoes conformational transition from an inert non-DNA-binding monomer to active functional trimers. HSBP1 is nuclear-localized and interacts with the active trimeric state of HSF1 to negatively regulate HSF1 DNA-binding activity. Overexpression of HSBP1 in mammalian cells represses the transactivation activity of HSF1. When overexpressed in C.elegans HSBP1 has severe effects on survival of the animals after thermal and chemical stress consistent with a role of HSBP1 as a negative regulator of heat shock response. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 16-83748390-A-C is Benign according to our data. Variant chr16-83748390-A-C is described in ClinVar as [Benign]. Clinvar id is 1285859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDH13NM_001257.5 linkuse as main transcriptc.1681+140A>C intron_variant ENST00000567109.6
CEDORAXR_007065143.1 linkuse as main transcriptn.142-12472T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDH13ENST00000567109.6 linkuse as main transcriptc.1681+140A>C intron_variant 1 NM_001257.5 P1P55290-1
CEDORAENST00000570056.2 linkuse as main transcriptn.142-19391T>G intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.0332
AC:
5053
AN:
152216
Hom.:
126
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00764
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.0341
Gnomad ASJ
AF:
0.0101
Gnomad EAS
AF:
0.0854
Gnomad SAS
AF:
0.0161
Gnomad FIN
AF:
0.0651
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.0413
Gnomad OTH
AF:
0.0287
GnomAD4 exome
AF:
0.0411
AC:
23360
AN:
568448
Hom.:
624
AF XY:
0.0402
AC XY:
11867
AN XY:
295136
show subpopulations
Gnomad4 AFR exome
AF:
0.00722
Gnomad4 AMR exome
AF:
0.0361
Gnomad4 ASJ exome
AF:
0.0128
Gnomad4 EAS exome
AF:
0.100
Gnomad4 SAS exome
AF:
0.0167
Gnomad4 FIN exome
AF:
0.0644
Gnomad4 NFE exome
AF:
0.0395
Gnomad4 OTH exome
AF:
0.0365
GnomAD4 genome
AF:
0.0332
AC:
5051
AN:
152334
Hom.:
126
Cov.:
32
AF XY:
0.0346
AC XY:
2575
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.00762
Gnomad4 AMR
AF:
0.0342
Gnomad4 ASJ
AF:
0.0101
Gnomad4 EAS
AF:
0.0856
Gnomad4 SAS
AF:
0.0157
Gnomad4 FIN
AF:
0.0651
Gnomad4 NFE
AF:
0.0413
Gnomad4 OTH
AF:
0.0284
Alfa
AF:
0.0369
Hom.:
14
Bravo
AF:
0.0299
Asia WGS
AF:
0.0430
AC:
150
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJun 18, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.53
DANN
Benign
0.67

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3743616; hg19: chr16-83781995; COSMIC: COSV51809761; API