rs13355121

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001291956.3(CDH18):​c.-580+138010C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,080 control chromosomes in the GnomAD database, including 3,799 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 ( 3799 hom., cov: 31)

Consequence

CDH18
NM_001291956.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110
Variant links:
Genes affected
CDH18 (HGNC:1757): (cadherin 18) This gene encodes a type II classical cadherin from the cadherin superfamily of integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. This particular cadherin is expressed specifically in the central nervous system and is putatively involved in synaptic adhesion, axon outgrowth and guidance. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDH18NM_001291956.3 linkuse as main transcriptc.-580+138010C>G intron_variant
CDH18NM_001349556.2 linkuse as main transcriptc.-434+138010C>G intron_variant
CDH18NM_001349558.2 linkuse as main transcriptc.-727-99213C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDH18ENST00000507958.5 linkuse as main transcriptc.-580+138010C>G intron_variant 2 P1Q13634-1
CDH18ENST00000507632.2 linkuse as main transcriptn.402+138010C>G intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.214
AC:
32280
AN:
150962
Hom.:
3798
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.175
Gnomad AMI
AF:
0.328
Gnomad AMR
AF:
0.135
Gnomad ASJ
AF:
0.149
Gnomad EAS
AF:
0.297
Gnomad SAS
AF:
0.234
Gnomad FIN
AF:
0.264
Gnomad MID
AF:
0.191
Gnomad NFE
AF:
0.242
Gnomad OTH
AF:
0.188
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.214
AC:
32295
AN:
151080
Hom.:
3799
Cov.:
31
AF XY:
0.212
AC XY:
15663
AN XY:
73770
show subpopulations
Gnomad4 AFR
AF:
0.175
Gnomad4 AMR
AF:
0.135
Gnomad4 ASJ
AF:
0.149
Gnomad4 EAS
AF:
0.297
Gnomad4 SAS
AF:
0.234
Gnomad4 FIN
AF:
0.264
Gnomad4 NFE
AF:
0.242
Gnomad4 OTH
AF:
0.187
Alfa
AF:
0.237
Hom.:
568
Bravo
AF:
0.203
Asia WGS
AF:
0.258
AC:
889
AN:
3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.39
DANN
Benign
0.68

Splicing

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: rs13355121; hg19: chr5-20437561; API