rs1479679

Variant summary

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

The NM_016279.4(CDH9):​c.1883-353A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0806 in 152,194 control chromosomes in the GnomAD database, including 716 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 0.081 ( 716 hom., cov: 32)

Consequence

CDH9
NM_016279.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.530
Variant links:
Genes affected
CDH9 (HGNC:1768): (cadherin 9) This gene encodes a type II classical cadherin from the cadherin superfamily, 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. The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity of the protein's homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDH9NM_016279.4 linkuse as main transcriptc.1883-353A>G intron_variant ENST00000231021.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDH9ENST00000231021.9 linkuse as main transcriptc.1883-353A>G intron_variant 1 NM_016279.4 P1
CDH9ENST00000505020.1 linkuse as main transcriptn.899-353A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0807
AC:
12268
AN:
152076
Hom.:
718
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0225
Gnomad AMI
AF:
0.215
Gnomad AMR
AF:
0.0859
Gnomad ASJ
AF:
0.145
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0217
Gnomad FIN
AF:
0.0590
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.124
Gnomad OTH
AF:
0.0817
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0806
AC:
12260
AN:
152194
Hom.:
716
Cov.:
32
AF XY:
0.0756
AC XY:
5626
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0225
Gnomad4 AMR
AF:
0.0857
Gnomad4 ASJ
AF:
0.145
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0213
Gnomad4 FIN
AF:
0.0590
Gnomad4 NFE
AF:
0.124
Gnomad4 OTH
AF:
0.0808
Alfa
AF:
0.107
Hom.:
461
Bravo
AF:
0.0814
Asia WGS
AF:
0.0120
AC:
43
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
4.7
DANN
Benign
0.33

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1479679; hg19: chr5-26882085; API