rs394241

Variant summary

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

The NM_004934.5(CDH18):​c.1253+11157C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0993 in 151,932 control chromosomes in the GnomAD database, including 1,040 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 0.099 ( 1040 hom., cov: 33)

Consequence

CDH18
NM_004934.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDH18NM_004934.5 linkuse as main transcriptc.1253+11157C>T intron_variant ENST00000382275.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDH18ENST00000382275.6 linkuse as main transcriptc.1253+11157C>T intron_variant 1 NM_004934.5 P1Q13634-1

Frequencies

GnomAD3 genomes
AF:
0.0991
AC:
15050
AN:
151814
Hom.:
1029
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.195
Gnomad AMI
AF:
0.00439
Gnomad AMR
AF:
0.0855
Gnomad ASJ
AF:
0.0710
Gnomad EAS
AF:
0.0966
Gnomad SAS
AF:
0.0431
Gnomad FIN
AF:
0.0473
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.0594
Gnomad OTH
AF:
0.0964
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0993
AC:
15094
AN:
151932
Hom.:
1040
Cov.:
33
AF XY:
0.0982
AC XY:
7292
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.195
Gnomad4 AMR
AF:
0.0857
Gnomad4 ASJ
AF:
0.0710
Gnomad4 EAS
AF:
0.0962
Gnomad4 SAS
AF:
0.0440
Gnomad4 FIN
AF:
0.0473
Gnomad4 NFE
AF:
0.0595
Gnomad4 OTH
AF:
0.0964
Alfa
AF:
0.0778
Hom.:
90
Bravo
AF:
0.108
Asia WGS
AF:
0.0850
AC:
296
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.1
DANN
Benign
0.26

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: rs394241; hg19: chr5-19560531; API